Pierrick Roger
| Snapshot Date: 2024-11-19 13:40 -0500 (Tue, 19 Nov 2024) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_20 |
| git_last_commit: e6b963e |
| git_last_commit_date: 2024-10-29 11:04:35 -0500 (Tue, 29 Oct 2024) |
| Back to Multiple platform build/check report for BioC 3.20: simplified long |
|
This page was generated on 2024-11-20 12:02 -0500 (Wed, 20 Nov 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| teran2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4481 |
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) | x86_64 | 4.4.2 (2024-10-31) -- "Pile of Leaves" | 4479 |
| palomino8 | Windows Server 2022 Datacenter | x64 | 4.4.2 (2024-10-31 ucrt) -- "Pile of Leaves" | 4359 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4539 |
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) | aarch64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4493 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 202/2289 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.12.0 (landing page) Pierrick Roger
| teran2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | | ||||||||
| nebbiolo2 | Linux (Ubuntu 24.04.1 LTS) / x86_64 | OK | OK | OK | ||||||||||
| palomino8 | Windows Server 2022 Datacenter / x64 | OK | OK | OK | OK | | ||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 22.03 LTS-SP1) / aarch64 | OK | OK | OK | ||||||||||
|
To the developers/maintainers of the biodbChebi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbChebi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbChebi |
| Version: 1.12.0 |
| Command: /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz |
| StartedAt: 2024-11-19 23:30:12 -0500 (Tue, 19 Nov 2024) |
| EndedAt: 2024-11-19 23:32:02 -0500 (Tue, 19 Nov 2024) |
| EllapsedTime: 109.5 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbChebi.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD check --install=check:biodbChebi.install-out.txt --library=/home/biocbuild/bbs-3.20-bioc/R/site-library --timings biodbChebi_1.12.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/meat/biodbChebi.Rcheck’
* using R version 4.4.2 (2024-10-31)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* checking for file ‘biodbChebi/DESCRIPTION’ ... OK
* this is package ‘biodbChebi’ version ‘1.12.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘biodbChebi’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.20-bioc/R/bin/R CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library ‘/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library’ * installing *source* package ‘biodbChebi’ ... ** using staged installation ** R ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbChebi)
biodbChebi.Rcheck/tests/testthat.Rout
R version 4.4.2 (2024-10-31) -- "Pile of Leaves"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # vi: fdm=marker
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbChebi)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbChebi")
biodb.INFO [2024-11-19 23:30:45.455][biodb::testContext]
biodb.INFO [2024-11-19 23:30:45.457][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:45.458][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-11-19 23:30:45.459][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:30:45.460][biodb::testContext]
biodb.INFO [2024-11-19 23:30:45.465][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:45.467][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:45.473][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:45.474][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:30:45.475][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:30:45.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.479][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:30:45.496][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:30:45.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.499][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.500][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:30:45.501][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:30:45.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.503][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.504][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:30:45.505][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:30:45.506][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:30:45.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.509][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.510][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:30:45.511][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:30:45.512][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:30:45.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.515][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:30:45.516][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:30:45.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.519][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.519][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:30:45.521][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:30:45.522][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:30:45.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.525][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:30:45.526][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:30:45.527][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.529][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:30:45.530][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:30:45.531][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:30:45.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.535][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:45.535][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:30:45.536][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:30:45.537][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:30:45.538][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:30:45.539][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:30:45.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.542][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:30:45.543][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:30:45.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.547][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:30:45.548][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:30:45.549][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.550][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[2024-11-19 23:30:45.551][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:30:45.552][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:30:45.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.556][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:30:45.557][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:30:45.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.560][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:30:45.561][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:30:45.562][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.563][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.564][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:30:45.565][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:30:45.569][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:30:45.570][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.571][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.572][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:30:45.573][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:30:45.574][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:30:45.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.577][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.580][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:30:45.613][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.635][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 23:30:45.636][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.637][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:45.637][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.638][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.639][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.640][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.640][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:45.641][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:45.642][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.642][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:30:45.643][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:45.644][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.645][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.645][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:45.645][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:45.645][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:45.645][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:45.645][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:45.646][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:45.647][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.647][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.648][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:45.649][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.649][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.650][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.651][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.651][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:45.652][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:45.653][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.653][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.654][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:30:45.656][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.656][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:45.657][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.658][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:45.659][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.659][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.660][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.661][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.661][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:45.662][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:45.663][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.663][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:30:45.664][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:45.665][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.665][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.666][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:45.666][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:45.666][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:45.666][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:30:45.666][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:30:45.667][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:45.668][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.668][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.669][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:45.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.671][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.672][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:45.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:45.673][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.674][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.675][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:30:45.676][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.677][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 23:30:45.677][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.678][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:45.679][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.679][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.680][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.681][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.681][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:30:45.682][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:45.683][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.683][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:30:45.684][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:45.685][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.685][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.686][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.687][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:45.687][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.688][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.689][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:45.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.691][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:45.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:45.693][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.694][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.695][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:30:45.696][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.697][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:30:45.697][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.698][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:45.699][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.699][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.700][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.701][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.701][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:30:45.702][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:45.703][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.704][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:30:45.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:45.705][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.706][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.706][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.707][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:30:45.708][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.708][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.709][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:45.710][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.710][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.711][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.711][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.712][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:45.713][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:45.713][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.714][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:30:45.717][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:45.717][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.721][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[2024-11-19 23:30:45.722][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.723][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.738][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.741][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.743][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[2024-11-19 23:30:45.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.752][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[2024-11-19 23:30:45.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.764][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.DEBUG[2024-11-19 23:30:45.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.771][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:30:45.774][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:30:45.775][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:30:45.776][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:30:45.777][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:30:45.778][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:30:45.779][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:45.780][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:45.781][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:30:45.782][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:30:45.783][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:45.784][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:30:45.785][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:30:45.786][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:30:45.787][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:30:45.788][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:30:45.789][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:30:45.790][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:30:45.791][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:30:45.792][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:30:45.793][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:30:45.794][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:30:45.795][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:30:45.796][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:30:45.797][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:30:45.798][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:30:45.799][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:30:45.800][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:30:45.801][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:30:45.801][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:30:45.802][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:30:45.803][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:30:45.804][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:30:45.805][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:30:45.806][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:30:45.807][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:30:45.808][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:30:45.809][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:30:45.815][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:30:45.816][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:30:45.817][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:30:45.818][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:30:45.819][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:30:45.820][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:30:45.821][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:30:45.822][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:30:45.823][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:30:45.824][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:30:45.825][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:30:45.826][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:30:45.827][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:30:45.828][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:30:45.829][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:30:45.830][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:30:45.831][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:30:45.832][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:30:45.833][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:30:45.834][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:30:45.835][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:30:45.836][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:30:45.837][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:30:45.838][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:30:45.839][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:30:45.840][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:30:45.841][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:30:45.842][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:30:45.843][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:30:45.844][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:30:45.845][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:30:45.846][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:30:45.847][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:30:45.848][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:30:45.849][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:30:45.850][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:30:45.851][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:30:45.852][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:30:45.853][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:30:45.854][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:30:45.855][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:30:45.856][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:30:45.857][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:30:45.858][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:30:45.859][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:30:45.863][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:30:45.864][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:30:45.866][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:30:45.867][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.868][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.868][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.872][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.874][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.875][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.883][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.883][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.885][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.DEBUG[2024-11-19 23:30:45.885][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.886][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.888][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.891][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.894][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.895][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.897][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[2024-11-19 23:30:45.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.902][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.915][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.915][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.917][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.921][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.922][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.923][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.925][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.927][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.928][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.930][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.932][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.933][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.934][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.935][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.936][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.937][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.938][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.938][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:30:45.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:45.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:45.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:45.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:45.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:45.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:45.946][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 23:30:45.953][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 23:30:45.954][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.955][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.956][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.956][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:30:45.957][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.958][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.958][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.959][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 23:30:45.960][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:30:45.960][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:30:45.961][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.962][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 23:30:45.963][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 23:30:45.964][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:30:45.965][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:30:45.965][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:30:45.965][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:30:45.966][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:30:45.966][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.967][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.968][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:30:45.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:30:45.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:30:45.970][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:30:45.970][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:30:45.970][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 23:30:45.971][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:30:45.972][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:30:45.972][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:30:45.973][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 23:30:45.973][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 23:30:45.977][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:30:45.978][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:30:45.979][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 23:30:45.980][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:30:45.982][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:30:45.983][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:30:46.004][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 23:30:46.005][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 23:30:46.007][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 23:30:46.010][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 23:30:46.013][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:46.014][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:30:46.015][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 23:30:46.015][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 23:30:46.022][biodb::testThat]
biodb.INFO [2024-11-19 23:30:46.023][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-11-19 23:30:46.023][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:46.024][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:46.027][loadFileContents] Loaded 1 files from cache: [1]: "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2024-11-19 23:30:46.029][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:46.031][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:30:46.037][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:46.038][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:46.038][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:46.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:46.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:46.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:46.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:46.057][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.058][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.060][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.073][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.074][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.074][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.075][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.094][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.097][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.098][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.099][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.100][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.103][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.104][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.105][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.105][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.106][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.109][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.110][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.111][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.111][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.112][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.115][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.116][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.117][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.117][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.118][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.121][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:46.122][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.123][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.124][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:46.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.127][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.128][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.129][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.129][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.130][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.133][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.134][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.135][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.135][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.137][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.139][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:46.140][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.141][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.142][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.143][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:46.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.145][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.146][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.147][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.148][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.149][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.151][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.163][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.166][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.169][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.207][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.212][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:46.215][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2024-11-19 23:30:46.217][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.220][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.221][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.245][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.247][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.250][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:46.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:46.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.253][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:46.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:46.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:46.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:46.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.259][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:46.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:46.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.273][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.299][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.308][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.311][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.314][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.331][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.332][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.332][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.333][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.334][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.342][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.371][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.374][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.377][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.378][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.379][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.380][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.392][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.394][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.397][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.399][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.399][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.400][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.408][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.411][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.414][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.417][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.417][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.418][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.419][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.419][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.427][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.433][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.436][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.436][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.438][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.438][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.440][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.449][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.454][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.455][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.456][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.457][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.457][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.465][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.468][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.471][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.473][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.474][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.475][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.476][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.484][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.487][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.490][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.492][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.493][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.494][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.495][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.503][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.506][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.509][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.511][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.512][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.513][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.514][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.522][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.525][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.533][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.535][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.536][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.537][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.538][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.538][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.546][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.552][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.555][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.556][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.557][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.565][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.568][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.571][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.574][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.574][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.576][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.576][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.584][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.585][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.586][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.589][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.590][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.591][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.594][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.595][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.597][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.600][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.600][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.602][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.605][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.606][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.607][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.610][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.611][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.612][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.615][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.616][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.617][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.621][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.621][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.623][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.626][ef$get] Asked field names are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.627][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.627][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.628][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.631][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.632][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.632][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.633][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.636][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.637][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.638][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.638][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:46.644][biodb::testThat]
biodb.INFO [2024-11-19 23:30:46.644][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-11-19 23:30:46.645][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:46.646][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:46.656][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2024-11-19 23:30:46.661][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:30:46.664][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2024-11-19 23:30:46.665][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:46.666][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2024-11-19 23:30:46.667][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:46.689][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:46.690][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:30:46.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:46.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:46.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:46.696][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:46.697][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:46.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:46.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:46.700][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.701][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.702][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.702][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.704][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.705][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.718][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.719][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.720][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.720][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.721][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:46.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:46.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.724][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.725][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.726][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.726][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.727][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:46.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:46.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.730][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.731][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.732][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.732][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.733][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:46.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:46.735][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.736][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.737][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.738][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.739][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:46.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.742][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.742][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.743][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.744][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.745][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:46.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.747][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:46.748][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.749][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.749][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.750][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:46.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:46.752][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.753][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.754][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.755][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.755][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.756][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:46.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.758][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.759][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.760][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.761][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.762][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.765][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:46.766][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.766][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.767][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.768][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:46.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:46.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.771][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.771][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.773][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.774][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:46.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:46.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.776][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.777][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.778][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.779][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.782][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.785][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:46.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.790][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.801][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:46.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:46.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:46.804][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2024-11-19 23:30:46.805][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-11-19 23:30:46.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-11-19 23:30:46.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.808][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-11-19 23:30:46.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-11-19 23:30:46.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.810][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-11-19 23:30:46.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-11-19 23:30:46.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:46.818][biodb::testThat]
biodb.INFO [2024-11-19 23:30:46.819][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-11-19 23:30:46.820][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:46.820][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:46.823][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.823][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.825][ef$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:46.826][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2024-11-19 23:30:46.849][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.852][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:46.854][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:46.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:46.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:46.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:46.859][function(conn, opt)] With value "squalene".
biodb.DEBUG[2024-11-19 23:30:46.862][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 23:30:46.877][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:30:46.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 23:30:46.889][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:46.890][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 23:30:46.906][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:30:46.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:46.909][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:46.910][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:30:47.540][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:30:48.094][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:48.097][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-19 23:30:48.108][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-19 23:30:48.110][function(conn, opt)] With found IDs [1]: "15440".
biodb.TRACE[2024-11-19 23:30:48.119][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.119][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:48.120][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.121][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.121][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.122][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.123][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.124][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:48.127][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.127][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-11-19 23:30:48.128][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:48.129][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:48.145][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.148][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.151][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:48.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:48.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:48.193][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:30:48.196][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:30:48.197][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 23:30:48.198][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:48.199][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2024-11-19 23:30:48.211][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.212][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-11-19 23:30:48.213][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:48.213][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:48.239][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.245][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.251][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.254][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.257][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.259][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.262][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:48.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:48.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.265][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:48.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:48.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.281][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.284][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:48.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:48.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.287][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.289][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:48.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.292][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.295][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:48.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.298][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.301][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-11-19 23:30:48.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.304][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:48.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-11-19 23:30:48.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:48.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:48.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-11-19 23:30:48.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:48.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:48.315][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.315][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-11-19 23:30:48.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:48.317][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.322][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.323][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-11-19 23:30:48.324][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:48.325][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.330][biodb::testThat]
biodb.INFO [2024-11-19 23:30:48.331][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-11-19 23:30:48.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:48.332][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:48.335][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2024-11-19 23:30:49.624][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2024-11-19 23:30:50.674][biodb::testThat]
biodb.INFO [2024-11-19 23:30:50.675][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-11-19 23:30:50.675][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:50.678][biodb::testThat]
biodb.DEBUG[2024-11-19 23:30:51.125][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/displayImage.do?defaultImage=true&imageIndex=0&chebiId=15440&dimensions=400.
biodb.TRACE[2024-11-19 23:30:51.585][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:51.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:51.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:51.588][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:51.589][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:51.590][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:51.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:51.604][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:30:51.605][biodb::testThat]
biodb.INFO [2024-11-19 23:30:51.606][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-11-19 23:30:51.607][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:30:51.607][biodb::testThat]
biodb.TRACE[2024-11-19 23:30:51.616][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:51.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:51.617][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:51.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:51.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:51.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:51.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:51.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:51.622][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:51.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:51.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:51.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:51.679][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:30:51.682][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:30:51.683][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 23:30:51.684][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:30:51.685][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 23:30:51.746][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.INFO [2024-11-19 23:30:51.749][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.DEBUG[2024-11-19 23:30:51.761][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:51.762][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:51.773][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:30:52.332][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:30:52.901][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:52.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-19 23:30:52.906][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.TRACE[2024-11-19 23:30:52.917][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:30:52.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:30:52.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.923][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.925][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.928][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.931][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:52.934][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:52.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:52.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:52.942][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:30:52.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:52.945][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:52.946][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:30:53.351][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:30:53.751][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2024-11-19 23:30:53.753][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2024-11-19 23:30:53.754][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2024-11-19 23:30:53.757][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2024-11-19 23:30:53.759][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:53.760][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.767][private$loadEntries] Creating entries from ids [1]: "192288".
biodb.DEBUG[2024-11-19 23:30:53.812][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:30:53.813][cch$loadFileContent] Trying to load 1 files from cache: [1]: "192288".
biodb.TRACE[2024-11-19 23:30:53.814][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:30:53.815][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:30:53.816][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:53.817][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:30:53.818][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:30:53.818][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:30:53.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:53.821][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:53.822][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:53.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:53.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:53.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:53.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:53.828][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.DEBUG[2024-11-19 23:30:53.830][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:53.831][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:53.832][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288".
biodb.TRACE[2024-11-19 23:30:54.234][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=192288).
biodb.DEBUG[2024-11-19 23:30:54.637][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:54.639][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.content"
biodb.TRACE[2024-11-19 23:30:54.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7e76f7a384ab933ed01801c92c3eec77.request"
biodb.TRACE[2024-11-19 23:30:54.644][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/192288.xml"
biodb.DEBUG[2024-11-19 23:30:54.645][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:30:54.646][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:54.647][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:30:54.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:54.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:54.650][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:54.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:54.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:54.655][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:54.656][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.TRACE[2024-11-19 23:30:54.658][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.659][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.659][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.660][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.661][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.664][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:54.665][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:54.665][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.666][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.667][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:54.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:54.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.670][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.671][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.671][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.672][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:54.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:54.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.676][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.677][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.678][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.678][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.679][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:54.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:54.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.682][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.683][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.683][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.684][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.685][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:54.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.688][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.689][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:54.689][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.690][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.691][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:54.692][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.692][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.693][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.694][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:54.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.697][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.697][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.698][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.699][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:54.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.702][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.703][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.704][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.704][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:54.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:54.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.708][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:54.709][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:54.710][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.710][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.711][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:54.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:54.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.714][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.715][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.716][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.716][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.717][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:54.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:54.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.720][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.721][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.723][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.725][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.726][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.728][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:54.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.731][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.734][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.775][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:54.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:54.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:54.781][self$createEntryFromContent] Accession numbers: 192288.
biodb.TRACE[2024-11-19 23:30:54.787][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.790][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:54.793][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:54.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:54.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:54.797][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:30:54.799][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:54.800][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:54.801][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:30:55.211][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:30:55.610][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:55.611][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2024-11-19 23:30:55.614][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2024-11-19 23:30:55.626][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.627][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.628][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.631][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.632][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.633][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.633][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:55.634][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:55.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:55.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.637][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:55.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:55.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:55.640][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:55.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:55.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:55.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:55.643][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.643][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.647][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.648][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.648][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:55.650][private$loadEntries] Creating entries from ids [1]: "209892".
biodb.DEBUG[2024-11-19 23:30:55.651][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:30:55.652][cch$loadFileContent] Trying to load 1 files from cache: [1]: "209892".
biodb.TRACE[2024-11-19 23:30:55.653][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:30:55.653][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:30:55.654][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:55.655][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:30:55.656][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:30:55.656][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:30:55.674][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:55.675][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:55.675][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:55.679][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:55.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:55.680][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:55.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:55.682][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.DEBUG[2024-11-19 23:30:55.684][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:55.685][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:55.686][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892".
biodb.TRACE[2024-11-19 23:30:56.089][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=209892).
biodb.DEBUG[2024-11-19 23:30:56.496][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:56.498][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.content"
biodb.TRACE[2024-11-19 23:30:56.502][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7a3362365076d47cdf0955cccdd37bcf.request"
biodb.TRACE[2024-11-19 23:30:56.504][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/209892.xml"
biodb.DEBUG[2024-11-19 23:30:56.505][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:30:56.506][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:56.507][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:30:56.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:56.509][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:56.510][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:56.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:56.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:56.515][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:56.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:56.518][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.519][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.524][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:56.525][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:56.525][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.526][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.527][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:56.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:56.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.530][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:56.531][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:56.531][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.532][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.533][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:56.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:56.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.536][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:56.537][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:56.538][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.538][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.539][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:56.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:56.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.542][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:56.543][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:56.544][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.544][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.545][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:56.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:56.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.548][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:56.549][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:56.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.550][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.551][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:56.552][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.553][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.553][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.554][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:56.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.557][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:56.558][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:56.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.559][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.560][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:56.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:56.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.563][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:56.564][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:56.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.565][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.566][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:56.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:56.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.569][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:56.570][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:56.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.571][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.572][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:56.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:56.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.575][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:56.576][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:56.577][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.577][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.578][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:56.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:56.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:56.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:56.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.584][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:56.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:56.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.587][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.590][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:56.590][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:56.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:56.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:56.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:56.967][self$createEntryFromContent] Accession numbers: 209892.
biodb.TRACE[2024-11-19 23:30:56.968][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.971][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:56.975][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:56.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:56.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:56.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:30:56.996][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:56.997][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:56.998][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:30:57.605][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:30:58.155][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:58.157][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2024-11-19 23:30:58.161][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2024-11-19 23:30:58.164][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:58.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:58.165][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:58.169][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:58.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:58.170][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:58.171][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:58.172][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:58.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:58.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:58.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:58.175][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:58.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:58.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:58.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:58.177][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:58.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:58.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:58.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:58.180][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:58.181][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:58.182][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:58.185][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:58.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:58.187][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:58.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:58.188][private$loadEntries] Creating entries from ids [1]: "26747".
biodb.DEBUG[2024-11-19 23:30:58.189][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:30:58.190][cch$loadFileContent] Trying to load 1 files from cache: [1]: "26747".
biodb.TRACE[2024-11-19 23:30:58.191][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:30:58.192][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:30:58.193][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:58.194][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:30:58.194][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:30:58.195][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:30:58.197][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:58.198][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:58.199][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:58.203][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:58.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:58.204][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:58.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:58.205][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.DEBUG[2024-11-19 23:30:58.208][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:58.208][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:58.210][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747".
biodb.TRACE[2024-11-19 23:30:58.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=26747).
biodb.DEBUG[2024-11-19 23:30:59.021][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:59.023][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.content"
biodb.TRACE[2024-11-19 23:30:59.025][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/462a35453014388bd90df1c9e4ade520.request"
biodb.TRACE[2024-11-19 23:30:59.027][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/26747.xml"
biodb.DEBUG[2024-11-19 23:30:59.028][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:30:59.029][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:59.030][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:30:59.032][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:59.032][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:59.033][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:59.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:59.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:59.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:59.039][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[2024-11-19 23:30:59.041][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.041][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.043][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.047][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:30:59.047][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:30:59.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.050][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:30:59.050][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:30:59.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.052][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.053][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:30:59.053][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:30:59.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.055][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.056][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:30:59.056][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:30:59.057][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.058][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.059][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:59.059][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:30:59.060][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.061][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.062][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:30:59.062][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.063][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.064][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.065][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:59.077][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:30:59.078][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.078][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.079][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:59.080][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:59.081][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.081][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.083][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:30:59.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:30:59.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.086][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:59.086][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:59.087][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.088][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.089][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:30:59.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:30:59.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.092][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:30:59.093][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:30:59.093][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.094][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:59.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:59.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.098][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:59.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:59.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.103][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:30:59.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:30:59.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.106][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.109][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.115][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.120][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:59.123][self$createEntryFromContent] Accession numbers: 26747.
biodb.TRACE[2024-11-19 23:30:59.124][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.129][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.130][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.131][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.131][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.133][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.136][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:30:59.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:30:59.139][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:59.140][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:59.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:59.145][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:59.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:59.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:59.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:59.147][private$loadEntries] Creating entries from ids [1]: "59285".
biodb.DEBUG[2024-11-19 23:30:59.148][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:30:59.150][cch$loadFileContent] Trying to load 1 files from cache: [1]: "59285".
biodb.TRACE[2024-11-19 23:30:59.150][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:30:59.151][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:30:59.152][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:30:59.153][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:30:59.154][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:30:59.154][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:30:59.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:59.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:59.158][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:59.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:59.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:59.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:59.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:30:59.164][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.DEBUG[2024-11-19 23:30:59.166][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:30:59.167][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:30:59.168][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285".
biodb.TRACE[2024-11-19 23:30:59.572][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=59285).
biodb.DEBUG[2024-11-19 23:30:59.974][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:30:59.977][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.content"
biodb.TRACE[2024-11-19 23:30:59.980][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a390fa120be311b7c431851d8d66d5ac.request"
biodb.TRACE[2024-11-19 23:30:59.982][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/59285.xml"
biodb.DEBUG[2024-11-19 23:30:59.983][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:30:59.984][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:30:59.985][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:30:59.986][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:30:59.987][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:30:59.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:30:59.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:30:59.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:30:59.993][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:30:59.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:30:59.996][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:30:59.997][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:30:59.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:30:59.998][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:30:59.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.002][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:00.003][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:00.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.004][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.005][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:00.006][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:00.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.007][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.008][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:00.009][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:00.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.010][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.011][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:00.012][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:00.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.022][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.023][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:00.024][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:00.024][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.025][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.026][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:00.027][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.028][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.029][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:00.030][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:00.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.031][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.032][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:00.033][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:00.034][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.034][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.036][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:00.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:00.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.038][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:00.039][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:00.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.041][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.041][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:00.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:00.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.044][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:00.045][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:00.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.046][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.047][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:00.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:00.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.050][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:00.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:00.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:00.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:00.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.067][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.070][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.073][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:00.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:00.076][self$createEntryFromContent] Accession numbers: 59285.
biodb.TRACE[2024-11-19 23:31:00.076][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.085][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:00.088][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:00.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:00.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:00.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:00.091][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:00.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:00.096][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:00.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:00.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:00.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:00.099][private$loadEntries] Creating entries from ids [1]: "75174".
biodb.DEBUG[2024-11-19 23:31:00.099][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:00.101][cch$loadFileContent] Trying to load 1 files from cache: [1]: "75174".
biodb.TRACE[2024-11-19 23:31:00.102][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:00.102][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:00.103][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:00.104][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:00.105][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:00.105][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:00.107][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:00.108][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:00.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:00.112][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:00.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:00.113][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:00.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:00.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.DEBUG[2024-11-19 23:31:00.117][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:00.118][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:00.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174".
biodb.TRACE[2024-11-19 23:31:00.572][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=75174).
biodb.DEBUG[2024-11-19 23:31:00.977][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:00.979][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.content"
biodb.TRACE[2024-11-19 23:31:00.983][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/379ec57940c7734782bc4c07c7e15a9b.request"
biodb.TRACE[2024-11-19 23:31:00.985][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/75174.xml"
biodb.DEBUG[2024-11-19 23:31:00.986][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:00.987][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:00.987][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:00.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:00.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:00.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:00.994][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:00.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:00.996][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:00.996][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[2024-11-19 23:31:00.998][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:00.999][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.000][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.001][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.004][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:01.005][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:01.014][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.015][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.016][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:01.017][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:01.017][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.019][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:01.020][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:01.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.021][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.022][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:01.023][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:01.023][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.024][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.025][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:01.026][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:01.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.027][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.028][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:01.029][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.030][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.031][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:01.032][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:01.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.033][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.034][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:01.035][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:01.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.036][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.037][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:01.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:01.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.040][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:01.041][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:01.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.042][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.043][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:01.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:01.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.046][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:01.047][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:01.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.048][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:01.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:01.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:01.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:01.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:01.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:01.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.071][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.074][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:01.077][self$createEntryFromContent] Accession numbers: 75174.
biodb.TRACE[2024-11-19 23:31:01.077][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.080][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.083][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.086][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:01.091][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:01.092][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:01.093][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:01.097][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:01.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:01.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:01.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:01.100][private$loadEntries] Creating entries from ids [1]: "15441".
biodb.DEBUG[2024-11-19 23:31:01.100][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:01.102][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15441".
biodb.TRACE[2024-11-19 23:31:01.102][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:01.103][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:01.104][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:01.105][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:01.105][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:01.106][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:01.108][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:01.109][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:01.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:01.113][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:01.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:01.114][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:01.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:01.115][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.DEBUG[2024-11-19 23:31:01.118][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:01.118][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:01.119][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441".
biodb.TRACE[2024-11-19 23:31:01.523][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15441).
biodb.DEBUG[2024-11-19 23:31:01.933][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:01.935][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.content"
biodb.TRACE[2024-11-19 23:31:01.938][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a6d4f93841bd82da498852b3a0a5692d.request"
biodb.TRACE[2024-11-19 23:31:01.940][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15441.xml"
biodb.DEBUG[2024-11-19 23:31:01.941][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:01.942][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:01.943][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:01.944][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:01.945][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:01.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:01.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:01.950][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:01.951][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:01.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:01.961][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.962][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.963][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.964][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:01.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:01.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.967][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:01.968][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:01.969][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.970][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.971][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:01.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:01.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.974][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:01.974][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:01.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.976][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.977][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:01.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:01.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.980][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:01.980][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:01.981][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.982][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.982][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:01.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:01.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.985][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:01.986][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:01.987][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.987][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.988][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:01.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:01.990][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.991][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:01.992][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:01.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.993][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.994][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:01.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:01.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:01.997][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:01.998][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:01.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:01.999][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.000][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:02.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.003][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.003][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.004][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.005][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.006][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.008][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:02.009][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:02.010][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.011][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:02.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:02.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.015][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:02.015][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:02.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.017][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.018][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:02.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:02.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.021][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:02.021][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:02.022][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.023][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.024][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:02.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:02.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.027][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:02.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:02.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:02.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:02.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.035][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:02.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:02.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.039][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.047][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.049][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.052][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.054][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.055][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:02.056][self$createEntryFromContent] Accession numbers: 15441.
biodb.TRACE[2024-11-19 23:31:02.056][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.059][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.062][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:02.065][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:02.065][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:02.066][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:02.070][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:02.071][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:02.072][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:02.072][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:02.073][private$loadEntries] Creating entries from ids [1]: "15442".
biodb.DEBUG[2024-11-19 23:31:02.074][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:02.075][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15442".
biodb.TRACE[2024-11-19 23:31:02.076][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:02.077][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:02.078][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:02.078][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:02.079][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:02.080][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:02.082][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:02.083][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:02.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:02.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:02.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:02.095][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:02.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:02.096][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.DEBUG[2024-11-19 23:31:02.098][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:02.099][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:02.100][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442".
biodb.TRACE[2024-11-19 23:31:02.504][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=15442).
biodb.DEBUG[2024-11-19 23:31:02.909][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:02.915][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.content"
biodb.TRACE[2024-11-19 23:31:02.922][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4c2c678eeeeb53d29ca6f3663ebee297.request"
biodb.TRACE[2024-11-19 23:31:02.924][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15442.xml"
biodb.DEBUG[2024-11-19 23:31:02.925][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:02.925][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:02.926][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:02.930][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:02.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:02.931][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:02.936][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:02.937][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:02.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:02.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:02.940][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.941][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.942][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.942][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:02.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:02.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.946][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:02.947][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:02.948][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.948][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.949][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:02.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:02.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.952][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:02.953][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:02.954][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.954][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.955][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:02.956][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:02.957][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.958][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:02.959][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:02.960][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.960][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.961][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:02.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:02.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.964][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:02.965][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:02.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.966][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.967][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:02.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:02.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.970][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:02.971][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:02.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.972][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.973][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:02.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:02.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.976][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:02.977][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.978][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.978][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.979][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:02.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:02.981][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.982][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.983][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.984][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.985][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:02.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.988][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:02.989][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:02.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.990][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.991][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:02.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:02.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.994][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:02.995][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:02.996][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.996][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:02.997][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:02.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:02.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:02.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.000][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:03.001][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:03.002][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.002][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.003][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:03.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:03.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:03.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.009][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:03.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:03.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.015][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:03.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:03.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.023][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.029][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.031][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.032][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:03.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:03.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:03.044][self$createEntryFromContent] Accession numbers: 15442.
biodb.TRACE[2024-11-19 23:31:03.045][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:03.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:03.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.048][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:03.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:03.049][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.050][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:03.051][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:03.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:03.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:03.053][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:03.054][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:03.054][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:03.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:03.059][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:03.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:03.060][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:03.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:03.062][private$loadEntries] Creating entries from ids [1]: "57310".
biodb.DEBUG[2024-11-19 23:31:03.062][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:03.064][cch$loadFileContent] Trying to load 1 files from cache: [1]: "57310".
biodb.TRACE[2024-11-19 23:31:03.065][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:03.065][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:03.066][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:03.067][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:03.068][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:03.068][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:03.070][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:03.071][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:03.072][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:03.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:03.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:03.076][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:03.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:03.078][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.DEBUG[2024-11-19 23:31:03.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:03.081][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:03.082][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310".
biodb.TRACE[2024-11-19 23:31:03.487][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=57310).
biodb.DEBUG[2024-11-19 23:31:04.036][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:04.038][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.content"
biodb.TRACE[2024-11-19 23:31:04.041][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e616043f98d9256021d0f5715e02d37b.request"
biodb.TRACE[2024-11-19 23:31:04.043][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/57310.xml"
biodb.DEBUG[2024-11-19 23:31:04.044][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:04.045][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:04.046][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:04.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:04.048][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:04.048][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:04.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:04.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:04.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:04.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:04.056][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.057][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.059][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.059][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.062][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:04.063][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:04.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.065][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.065][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:04.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:04.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.068][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:04.069][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:04.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.071][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.071][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:04.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:04.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.074][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:04.075][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:04.076][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.076][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.077][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:04.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:04.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.080][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:04.081][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:04.082][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.082][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.083][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:04.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:04.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.086][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:04.087][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:04.088][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.088][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.089][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:04.090][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.091][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.092][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:04.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.095][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:04.096][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:04.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.097][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.098][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:04.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:04.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.101][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:04.102][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:04.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.103][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.104][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:04.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:04.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.107][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:04.108][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:04.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.109][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.110][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:04.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:04.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.113][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:04.114][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:04.114][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.115][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.116][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:04.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:04.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.119][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:04.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:04.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.122][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:04.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:04.123][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.133][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.136][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:04.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:04.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.143][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.144][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.145][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.149][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.150][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.154][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:04.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:04.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:04.157][self$createEntryFromContent] Accession numbers: 57310.
biodb.TRACE[2024-11-19 23:31:04.158][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.160][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:04.163][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:04.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:04.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:04.166][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:04.167][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:04.167][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:04.171][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:04.172][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:04.172][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:04.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:04.174][private$loadEntries] Creating entries from ids [1]: "66216".
biodb.DEBUG[2024-11-19 23:31:04.175][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:04.176][cch$loadFileContent] Trying to load 1 files from cache: [1]: "66216".
biodb.TRACE[2024-11-19 23:31:04.177][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:04.178][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:04.178][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:04.179][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:04.180][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:04.181][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:04.183][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:04.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:04.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:04.187][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:04.188][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:04.188][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:04.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:04.190][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.DEBUG[2024-11-19 23:31:04.192][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:04.193][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:04.194][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216".
biodb.TRACE[2024-11-19 23:31:04.599][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=66216).
biodb.DEBUG[2024-11-19 23:31:05.006][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:05.009][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.content"
biodb.TRACE[2024-11-19 23:31:05.012][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a59039263bdeb010b063b31b1dcdd109.request"
biodb.TRACE[2024-11-19 23:31:05.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/66216.xml"
biodb.DEBUG[2024-11-19 23:31:05.015][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:05.016][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:05.017][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:05.018][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:05.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:05.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:05.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:05.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:05.025][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:05.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:05.028][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.029][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.029][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.030][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.034][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:05.035][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:05.035][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.036][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.037][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:05.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:05.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.040][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:05.041][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:05.041][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.042][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.043][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:05.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:05.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.046][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:05.046][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:05.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.048][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.049][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:05.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:05.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.052][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:05.052][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:05.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.054][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.055][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:05.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:05.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.058][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:05.058][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:05.059][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.060][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.061][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:05.061][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.062][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.063][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.063][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:05.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.066][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:05.067][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:05.068][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.069][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.069][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:05.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.081][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:05.082][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:05.083][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.083][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.084][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:05.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:05.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.087][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:05.088][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:05.089][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.090][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.090][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:05.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:05.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.094][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:05.094][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:05.095][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.096][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.097][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:05.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:05.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:05.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:05.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:05.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:05.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.105][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.106][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.107][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.108][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:05.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:05.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.111][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.114][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.116][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.119][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:05.128][self$createEntryFromContent] Accession numbers: 66216.
biodb.TRACE[2024-11-19 23:31:05.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.134][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:05.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:05.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:05.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:05.138][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:05.142][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:05.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:05.144][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:05.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:05.145][private$loadEntries] Creating entries from ids [1]: "70860".
biodb.DEBUG[2024-11-19 23:31:05.146][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:05.147][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70860".
biodb.TRACE[2024-11-19 23:31:05.148][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:05.149][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:05.150][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:05.150][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:05.151][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:05.152][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:05.154][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:05.155][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:05.155][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:05.158][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:05.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:05.160][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:05.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:05.161][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.DEBUG[2024-11-19 23:31:05.163][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:05.164][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:05.165][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860".
biodb.TRACE[2024-11-19 23:31:05.566][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70860).
biodb.DEBUG[2024-11-19 23:31:05.969][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:05.971][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.content"
biodb.TRACE[2024-11-19 23:31:05.973][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/02f38adb5262f39c1de7b27972a97d3a.request"
biodb.TRACE[2024-11-19 23:31:05.975][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70860.xml"
biodb.DEBUG[2024-11-19 23:31:05.976][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:05.977][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:05.978][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:05.979][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:05.980][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:05.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:05.984][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:05.985][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:05.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:05.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:05.988][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.988][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.989][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.990][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.991][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:05.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:05.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.994][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:05.994][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:05.995][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.996][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:05.997][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:05.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:05.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:05.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.000][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:06.000][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:06.001][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.002][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.003][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:06.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:06.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:06.006][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:06.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.016][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.017][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:06.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:06.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.020][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:06.021][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:06.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.022][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.023][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:06.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:06.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.026][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:06.027][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:06.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.028][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.029][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:06.030][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.031][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.032][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:06.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.035][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:06.036][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:06.036][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.037][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.038][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:06.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:06.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.040][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:06.041][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:06.042][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.043][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.043][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:06.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:06.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.046][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:06.047][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:06.048][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.048][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.049][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:06.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:06.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.052][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:06.053][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:06.054][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.054][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.055][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:06.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:06.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.058][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:06.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:06.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:06.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:06.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.064][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:06.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:06.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.069][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.078][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.081][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:06.086][self$createEntryFromContent] Accession numbers: 70860.
biodb.TRACE[2024-11-19 23:31:06.087][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.090][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.093][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:06.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:06.096][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:06.096][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:06.097][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:06.101][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:06.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:06.102][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:06.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:06.103][private$loadEntries] Creating entries from ids [1]: "70861".
biodb.DEBUG[2024-11-19 23:31:06.104][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:06.105][cch$loadFileContent] Trying to load 1 files from cache: [1]: "70861".
biodb.TRACE[2024-11-19 23:31:06.106][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:06.107][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:06.108][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:06.109][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:06.109][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:06.110][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:06.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:06.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:06.113][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:06.117][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:06.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:06.118][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:06.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:06.120][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.DEBUG[2024-11-19 23:31:06.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:06.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:06.124][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861".
biodb.TRACE[2024-11-19 23:31:06.525][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=70861).
biodb.DEBUG[2024-11-19 23:31:06.930][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:06.932][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.content"
biodb.TRACE[2024-11-19 23:31:06.935][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2469ce985de4364ded27031736786fb4.request"
biodb.TRACE[2024-11-19 23:31:06.937][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70861.xml"
biodb.DEBUG[2024-11-19 23:31:06.938][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:06.939][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:06.940][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:06.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:06.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:06.942][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:06.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:06.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:06.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:06.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:06.986][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.987][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.988][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.988][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.989][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:06.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:06.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.992][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:06.993][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:06.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.995][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.996][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:06.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:06.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:06.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:06.999][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:06.999][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:07.000][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.001][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.002][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:07.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:07.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.005][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:07.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:07.006][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.007][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.007][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:07.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:07.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.010][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:07.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:07.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.012][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:07.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:07.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.016][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:07.017][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:07.018][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.018][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.019][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:07.020][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.021][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.021][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.022][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.025][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:07.026][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:07.027][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.027][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.028][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:07.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:07.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.031][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:07.032][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:07.033][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.033][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.034][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:07.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:07.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.037][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:07.038][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:07.039][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.039][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.040][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:07.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:07.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.043][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:07.044][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:07.044][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.045][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.046][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:07.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:07.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.049][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:07.050][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:07.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.052][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:07.053][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:07.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.055][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.057][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:07.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:07.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.066][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.072][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.075][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:07.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:07.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:07.078][self$createEntryFromContent] Accession numbers: 70861.
biodb.TRACE[2024-11-19 23:31:07.079][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.082][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:07.084][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:07.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:07.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:07.087][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:07.088][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:07.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:07.093][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:07.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:07.094][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:07.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:07.095][private$loadEntries] Creating entries from ids [1]: "78662".
biodb.DEBUG[2024-11-19 23:31:07.096][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:07.097][cch$loadFileContent] Trying to load 1 files from cache: [1]: "78662".
biodb.TRACE[2024-11-19 23:31:07.098][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:07.099][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:07.100][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:07.101][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:07.101][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:07.102][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:07.104][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:07.105][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:07.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:07.114][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:07.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:07.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:07.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:07.118][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.DEBUG[2024-11-19 23:31:07.120][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:07.120][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:07.121][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662".
biodb.TRACE[2024-11-19 23:31:07.527][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=78662).
biodb.DEBUG[2024-11-19 23:31:08.232][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:08.234][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.content"
biodb.TRACE[2024-11-19 23:31:08.236][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2a2164b6127ca54c00efe5984f5864a.request"
biodb.TRACE[2024-11-19 23:31:08.238][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/78662.xml"
biodb.DEBUG[2024-11-19 23:31:08.239][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:08.240][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:08.241][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:08.243][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:08.243][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:08.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:08.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:08.248][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:08.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:08.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:08.252][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.252][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.253][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.254][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.258][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:08.258][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:08.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.260][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.261][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:08.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:08.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.264][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:08.265][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:08.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.266][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:08.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:08.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.270][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:08.271][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:08.271][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.272][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.273][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:08.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:08.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.276][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:08.277][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:08.277][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.278][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.279][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:08.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:08.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.282][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:08.283][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:08.283][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.284][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.285][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:08.286][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.287][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.288][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:08.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.291][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:08.292][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:08.292][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.293][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.294][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:08.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:08.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.297][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:08.298][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:08.298][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.299][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:08.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:08.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.303][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:08.304][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:08.304][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.305][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.306][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:08.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:08.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.309][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:08.310][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:08.310][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.311][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.312][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:08.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:08.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.315][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:08.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:08.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.318][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:08.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:08.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.321][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.323][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:08.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:08.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.329][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.335][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.337][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.340][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:08.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:08.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:08.343][self$createEntryFromContent] Accession numbers: 78662.
biodb.TRACE[2024-11-19 23:31:08.344][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.347][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:08.358][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:08.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:08.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:08.361][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:08.362][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:08.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:08.367][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:08.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:08.368][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:08.369][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:08.370][private$loadEntries] Creating entries from ids [1]: "85084".
biodb.DEBUG[2024-11-19 23:31:08.370][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:08.372][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85084".
biodb.TRACE[2024-11-19 23:31:08.373][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:08.373][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:08.374][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:08.375][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:08.376][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:08.376][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:08.378][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:08.379][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:08.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:08.383][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:08.383][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:08.384][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:08.385][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:08.386][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.DEBUG[2024-11-19 23:31:08.388][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:08.388][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:08.389][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084".
biodb.TRACE[2024-11-19 23:31:08.790][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85084).
biodb.DEBUG[2024-11-19 23:31:09.190][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:09.192][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.content"
biodb.TRACE[2024-11-19 23:31:09.194][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62216dc29cd0685dbac0a61545bda088.request"
biodb.TRACE[2024-11-19 23:31:09.196][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85084.xml"
biodb.DEBUG[2024-11-19 23:31:09.197][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:09.198][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:09.199][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:09.200][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:09.201][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:09.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:09.205][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:09.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:09.206][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:09.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:09.208][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.209][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.210][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.211][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.214][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:09.215][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:09.216][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.216][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.217][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:09.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:09.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.220][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:09.221][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:09.222][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.222][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.223][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:09.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:09.225][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.226][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:09.227][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:09.228][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.228][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.229][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:09.230][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:09.231][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.231][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.232][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:09.233][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:09.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.234][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.235][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:09.236][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.238][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:09.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.241][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:09.242][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:09.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.243][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.244][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:09.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:09.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.247][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:09.248][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:09.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.249][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.250][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:09.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:09.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.253][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:09.254][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:09.255][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.256][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.256][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:09.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:09.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.259][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:09.260][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:09.261][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.261][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:09.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:09.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.265][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:09.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:09.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.271][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:09.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:09.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.294][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:09.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:09.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:09.300][self$createEntryFromContent] Accession numbers: 85084.
biodb.TRACE[2024-11-19 23:31:09.301][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.304][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:09.307][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:09.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:09.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:09.310][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:09.310][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:09.311][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:09.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:09.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:09.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:09.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:09.318][private$loadEntries] Creating entries from ids [1]: "85086".
biodb.DEBUG[2024-11-19 23:31:09.318][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:09.320][cch$loadFileContent] Trying to load 1 files from cache: [1]: "85086".
biodb.TRACE[2024-11-19 23:31:09.320][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:09.321][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:09.322][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:09.323][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:09.323][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:09.324][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:09.326][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:09.327][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:09.328][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:09.331][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:09.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:09.332][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:09.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:09.334][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.DEBUG[2024-11-19 23:31:09.336][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:09.337][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:09.338][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086".
biodb.TRACE[2024-11-19 23:31:09.738][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=85086).
biodb.DEBUG[2024-11-19 23:31:10.144][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:10.146][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.content"
biodb.TRACE[2024-11-19 23:31:10.150][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/cf3472363c4a7effe355d93315025f8b.request"
biodb.TRACE[2024-11-19 23:31:10.152][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/85086.xml"
biodb.DEBUG[2024-11-19 23:31:10.153][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:10.154][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:10.155][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:10.156][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:10.157][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:10.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:10.161][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:10.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:10.162][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:10.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:10.165][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.166][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.167][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.167][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.168][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.171][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:10.172][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:10.173][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.173][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.174][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:10.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:10.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.177][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:10.178][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:10.179][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.179][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:10.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:10.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.183][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:10.184][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:10.185][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.185][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.186][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:10.187][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:10.188][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.188][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.189][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:10.190][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:10.191][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.191][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.192][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:10.193][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.194][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.194][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.195][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:10.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.198][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:10.199][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:10.200][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.200][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:10.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:10.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.204][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:10.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:10.206][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.206][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.207][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:10.208][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:10.209][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.210][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.210][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:10.211][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:10.212][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.212][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.213][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:10.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:10.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.216][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:10.217][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:10.218][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.218][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.219][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:10.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:10.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.222][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:10.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:10.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.237][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:10.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:10.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.246][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.249][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:10.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:10.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.257][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:10.258][self$createEntryFromContent] Accession numbers: 85086.
biodb.TRACE[2024-11-19 23:31:10.259][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.262][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:10.264][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:10.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:10.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:10.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:10.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:10.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:10.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:10.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:10.273][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:10.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:10.275][private$loadEntries] Creating entries from ids [1]: "88123".
biodb.DEBUG[2024-11-19 23:31:10.276][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:10.277][cch$loadFileContent] Trying to load 1 files from cache: [1]: "88123".
biodb.TRACE[2024-11-19 23:31:10.278][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:10.279][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:10.279][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:10.280][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:10.281][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:10.281][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:10.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:10.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:10.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:10.288][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:10.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:10.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:10.290][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:10.291][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.DEBUG[2024-11-19 23:31:10.293][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:10.294][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:10.295][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123".
biodb.TRACE[2024-11-19 23:31:10.701][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=88123).
biodb.DEBUG[2024-11-19 23:31:11.271][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:11.274][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.content"
biodb.TRACE[2024-11-19 23:31:11.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8e37f256f660b350650d4ca45d7cd291.request"
biodb.TRACE[2024-11-19 23:31:11.279][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/88123.xml"
biodb.DEBUG[2024-11-19 23:31:11.280][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:11.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:11.282][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:11.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:11.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:11.284][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:11.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:11.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:11.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:11.291][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[2024-11-19 23:31:11.292][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.293][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.294][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.295][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.298][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:11.299][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:11.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.301][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.302][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:11.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:11.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.304][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:11.305][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:11.306][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.307][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:11.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:11.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.310][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:11.312][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:11.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:11.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:11.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:11.318][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:11.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:11.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:11.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.323][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:11.324][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:11.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.325][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.326][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:11.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.327][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.328][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.329][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:11.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.332][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:11.332][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:11.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.334][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.335][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:11.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:11.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.338][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:11.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:11.345][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.350][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:11.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:11.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.354][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:11.355][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:11.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.357][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.357][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:11.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:11.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.360][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:11.361][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:11.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.363][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.364][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:11.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:11.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:11.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:11.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.370][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:11.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:11.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.372][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.375][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:11.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:11.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:11.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:11.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:11.395][self$createEntryFromContent] Accession numbers: 88123.
biodb.TRACE[2024-11-19 23:31:11.396][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:11.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:11.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:11.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:11.405][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:11.406][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:11.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:11.410][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:11.411][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:11.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:11.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:11.413][private$loadEntries] Creating entries from ids [1]: "134117".
biodb.DEBUG[2024-11-19 23:31:11.414][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:11.415][cch$loadFileContent] Trying to load 1 files from cache: [1]: "134117".
biodb.TRACE[2024-11-19 23:31:11.416][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:11.417][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:11.417][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:11.418][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:11.419][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:11.420][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:11.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:11.422][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:11.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:11.426][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:11.427][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:11.428][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:11.428][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:11.429][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.DEBUG[2024-11-19 23:31:11.431][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:11.432][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:11.433][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117".
biodb.TRACE[2024-11-19 23:31:11.836][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=134117).
biodb.DEBUG[2024-11-19 23:31:12.242][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:12.244][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.content"
biodb.TRACE[2024-11-19 23:31:12.246][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/8f998f0023bf19b8745b926f0b2992d7.request"
biodb.TRACE[2024-11-19 23:31:12.248][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/134117.xml"
biodb.DEBUG[2024-11-19 23:31:12.249][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:12.250][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:12.251][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:12.253][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:12.253][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:12.254][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:12.258][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:12.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:12.259][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:12.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:12.262][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.262][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.264][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.268][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:12.268][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:12.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.270][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.271][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:12.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:12.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.273][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:12.274][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:12.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.275][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.276][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:12.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:12.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.279][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:12.280][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:12.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.281][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.282][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:12.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:12.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.294][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:12.295][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:12.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.296][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.297][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:12.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:12.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.300][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:12.301][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:12.302][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.303][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.303][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:12.304][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.306][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.307][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:12.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.310][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:12.311][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:12.311][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.312][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:12.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:12.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.316][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:12.316][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:12.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.318][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.319][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:12.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:12.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.322][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:12.322][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:12.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.324][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.324][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:12.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:12.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.327][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:12.328][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:12.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.329][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.330][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:12.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:12.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:12.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:12.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.336][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:12.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:12.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.339][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.341][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:12.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:12.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.347][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.350][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:12.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:12.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:12.361][self$createEntryFromContent] Accession numbers: 134117.
biodb.TRACE[2024-11-19 23:31:12.362][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.365][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:12.368][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:12.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:12.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:12.371][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:12.371][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:12.372][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:12.376][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:12.376][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:12.377][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:12.378][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:12.378][private$loadEntries] Creating entries from ids [1]: "138307".
biodb.DEBUG[2024-11-19 23:31:12.379][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:12.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "138307".
biodb.TRACE[2024-11-19 23:31:12.381][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:12.382][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:12.383][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:12.384][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:12.384][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:12.385][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:12.387][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:12.388][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:12.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:12.391][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:12.392][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:12.393][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:12.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:12.394][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.DEBUG[2024-11-19 23:31:12.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:12.397][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:12.398][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307".
biodb.TRACE[2024-11-19 23:31:12.800][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=138307).
biodb.DEBUG[2024-11-19 23:31:13.202][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:13.204][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.content"
biodb.TRACE[2024-11-19 23:31:13.206][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/a2610bdf009c6327ccf7d519fff16ded.request"
biodb.TRACE[2024-11-19 23:31:13.208][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/138307.xml"
biodb.DEBUG[2024-11-19 23:31:13.209][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:13.210][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:13.211][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:13.212][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:13.213][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:13.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:13.217][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:13.217][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:13.218][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:13.219][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[2024-11-19 23:31:13.226][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.229][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.230][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.231][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.232][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.233][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.235][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:13.236][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:13.237][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.238][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:13.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:13.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.241][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:13.242][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:13.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.243][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.244][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:13.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:13.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.247][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:13.248][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:13.249][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.249][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.250][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:13.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:13.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.253][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:13.254][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:13.254][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.255][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.256][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:13.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:13.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.259][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:13.259][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:13.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.261][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.262][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:13.262][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.264][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.264][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:13.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.267][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:13.268][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:13.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.269][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.270][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:13.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:13.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.273][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:13.274][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:13.274][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.275][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.276][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:13.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:13.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.279][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:13.280][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:13.280][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.281][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.282][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:13.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:13.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.285][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:13.285][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:13.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.287][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.288][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:13.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:13.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.290][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:13.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:13.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.293][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:13.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:13.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.299][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:13.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:13.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.301][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.304][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.313][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:13.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:13.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:13.319][self$createEntryFromContent] Accession numbers: 138307.
biodb.TRACE[2024-11-19 23:31:13.320][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.323][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:13.325][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:13.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:13.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:13.328][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:13.329][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:13.329][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:13.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:13.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:13.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:13.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:13.477][private$loadEntries] Creating entries from ids [1]: "176803".
biodb.DEBUG[2024-11-19 23:31:13.478][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:13.479][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176803".
biodb.TRACE[2024-11-19 23:31:13.480][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:13.481][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:13.482][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:13.482][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:13.483][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:13.484][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:13.486][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:13.486][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:13.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:13.490][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:13.491][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:13.492][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:13.492][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:13.499][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.DEBUG[2024-11-19 23:31:13.501][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:13.502][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:13.503][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803".
biodb.TRACE[2024-11-19 23:31:13.904][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176803).
biodb.DEBUG[2024-11-19 23:31:14.308][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:14.310][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.content"
biodb.TRACE[2024-11-19 23:31:14.313][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/648921bf283f148f1437569ccee0fc41.request"
biodb.TRACE[2024-11-19 23:31:14.314][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176803.xml"
biodb.DEBUG[2024-11-19 23:31:14.316][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:14.317][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:14.318][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:14.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:14.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:14.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:14.324][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:14.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:14.325][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:14.326][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[2024-11-19 23:31:14.328][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.329][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.329][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.330][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.331][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.334][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:14.335][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:14.335][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.336][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.337][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:14.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:14.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.340][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:14.341][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:14.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.342][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.343][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:14.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:14.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.346][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:14.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:14.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.348][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.349][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:14.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:14.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.352][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:14.353][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:14.353][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.354][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.355][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:14.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:14.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.358][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:14.358][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:14.359][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.360][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.361][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:14.361][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.362][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.363][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.364][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:14.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.367][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:14.367][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:14.368][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.369][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.369][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:14.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:14.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.372][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:14.373][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:14.374][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.374][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:14.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:14.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.378][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:14.379][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:14.380][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.380][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.381][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:14.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:14.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.384][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:14.385][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:14.385][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.386][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.387][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:14.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:14.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.390][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:14.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:14.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.393][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:14.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:14.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.398][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:14.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:14.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.404][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.407][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.410][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:14.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:14.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:14.418][self$createEntryFromContent] Accession numbers: 176803.
biodb.TRACE[2024-11-19 23:31:14.419][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.421][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.422][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:14.424][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:14.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:14.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:14.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:14.437][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:14.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:14.441][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:14.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:14.443][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:14.443][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:14.444][private$loadEntries] Creating entries from ids [1]: "176962".
biodb.DEBUG[2024-11-19 23:31:14.445][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:14.446][cch$loadFileContent] Trying to load 1 files from cache: [1]: "176962".
biodb.TRACE[2024-11-19 23:31:14.447][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:14.448][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:14.449][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:14.450][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:14.450][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:14.451][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:14.453][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:14.454][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:14.454][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:14.458][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:14.458][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:14.459][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:14.460][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:14.461][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.DEBUG[2024-11-19 23:31:14.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:14.463][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:14.464][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962".
biodb.TRACE[2024-11-19 23:31:14.864][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=176962).
biodb.DEBUG[2024-11-19 23:31:15.271][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:15.272][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.content"
biodb.TRACE[2024-11-19 23:31:15.274][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/881a0b9df4a64ff0258c2dc68959eb26.request"
biodb.TRACE[2024-11-19 23:31:15.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/176962.xml"
biodb.DEBUG[2024-11-19 23:31:15.277][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:15.278][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:15.279][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:15.280][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:15.281][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:15.282][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:15.285][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:15.286][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:15.286][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:15.287][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[2024-11-19 23:31:15.289][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.290][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.291][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.292][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.295][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:15.296][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:15.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.297][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.298][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:15.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:15.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.304][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:15.304][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:15.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.306][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.307][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:15.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:15.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.310][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:15.311][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:15.312][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:15.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:15.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:15.318][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:15.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:15.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:15.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.323][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:15.324][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:15.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.325][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.326][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:15.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.328][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.329][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:15.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:15.334][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:15.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.335][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:15.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:15.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.339][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:15.340][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:15.341][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.342][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:15.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:15.344][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.345][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.346][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:15.347][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:15.347][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.348][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.349][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:15.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:15.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.352][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:15.353][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:15.354][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.354][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.355][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:15.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:15.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.358][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:15.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:15.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.362][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:15.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:15.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:15.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:15.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.395][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.402][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:15.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:15.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:15.405][self$createEntryFromContent] Accession numbers: 176962.
biodb.TRACE[2024-11-19 23:31:15.406][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.409][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:15.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:15.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:15.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:15.415][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:15.416][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:15.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:15.422][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:15.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:15.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:15.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:15.425][private$loadEntries] Creating entries from ids [1]: "198655".
biodb.DEBUG[2024-11-19 23:31:15.426][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:15.427][cch$loadFileContent] Trying to load 1 files from cache: [1]: "198655".
biodb.TRACE[2024-11-19 23:31:15.429][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:15.429][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:15.430][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:15.431][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:15.432][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:15.433][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:15.436][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:15.436][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:15.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:15.442][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:15.443][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:15.444][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:15.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:15.446][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.DEBUG[2024-11-19 23:31:15.449][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:15.450][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:15.451][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655".
biodb.TRACE[2024-11-19 23:31:15.857][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=198655).
biodb.DEBUG[2024-11-19 23:31:16.270][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:16.273][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.content"
biodb.TRACE[2024-11-19 23:31:16.276][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/f2e175d021d3c86c1362fa584a90fbad.request"
biodb.TRACE[2024-11-19 23:31:16.279][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/198655.xml"
biodb.DEBUG[2024-11-19 23:31:16.280][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:16.281][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:16.282][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:16.283][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:16.284][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:16.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:16.289][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:16.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:16.290][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:16.291][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[2024-11-19 23:31:16.293][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.294][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.295][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.295][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.299][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:16.300][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:16.301][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.301][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.302][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:16.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:16.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.305][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:16.306][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:16.307][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.307][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.308][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:16.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:16.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.311][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:16.312][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:16.313][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.313][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.314][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:16.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:16.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.317][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:16.318][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:16.319][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.319][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.320][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:16.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:16.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.323][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:16.324][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:16.325][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.326][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.327][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:16.327][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.328][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.329][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.330][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:16.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.333][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:16.333][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:16.334][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.335][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.336][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:16.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:16.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.338][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:16.339][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:16.340][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.340][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:16.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:16.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.344][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:16.345][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:16.346][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.358][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.360][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:16.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:16.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.363][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:16.364][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:16.365][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.365][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.366][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:16.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:16.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.369][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:16.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:16.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:16.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:16.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.376][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.378][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:16.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:16.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.387][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.396][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:16.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:16.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:16.398][self$createEntryFromContent] Accession numbers: 198655.
biodb.TRACE[2024-11-19 23:31:16.399][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.402][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:16.405][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:16.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:16.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:16.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:16.409][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:16.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:16.414][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:16.414][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:16.415][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:16.416][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:16.417][private$loadEntries] Creating entries from ids [1]: "215045".
biodb.DEBUG[2024-11-19 23:31:16.417][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:16.419][cch$loadFileContent] Trying to load 1 files from cache: [1]: "215045".
biodb.TRACE[2024-11-19 23:31:16.420][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:16.420][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:16.421][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:16.422][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:16.423][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:16.423][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:16.426][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:16.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:16.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:16.431][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:16.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:16.432][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:16.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:16.434][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.DEBUG[2024-11-19 23:31:16.436][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:16.437][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:16.438][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045".
biodb.TRACE[2024-11-19 23:31:16.842][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=215045).
biodb.DEBUG[2024-11-19 23:31:17.248][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:17.250][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.content"
biodb.TRACE[2024-11-19 23:31:17.253][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/5fb598055294db64f197c61a6e36b01a.request"
biodb.TRACE[2024-11-19 23:31:17.255][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/215045.xml"
biodb.DEBUG[2024-11-19 23:31:17.257][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:17.258][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:17.259][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:17.260][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.261][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.266][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.268][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.270][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.271][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.273][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.274][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.277][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:17.278][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:17.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.279][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.280][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:17.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:17.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.283][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:17.284][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:17.285][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.285][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.286][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:17.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:17.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:17.290][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:17.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.291][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.292][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:17.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:17.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.295][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:17.296][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:17.297][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.297][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.298][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:17.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:17.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.312][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:17.313][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:17.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.315][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.316][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:17.317][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.318][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.318][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.319][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:17.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.322][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.323][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.324][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.325][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.326][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.329][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:17.329][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:17.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.331][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.332][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:17.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:17.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.335][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:17.336][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:17.336][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.337][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.338][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:17.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:17.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.341][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:17.341][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:17.342][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.343][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.344][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:17.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:17.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.347][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:17.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:17.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.350][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:17.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:17.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.353][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.356][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:17.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:17.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.362][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.373][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:17.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:17.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.375][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.376][self$createEntryFromContent] Accession numbers: 215045.
biodb.TRACE[2024-11-19 23:31:17.377][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.380][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.383][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.400][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:17.402][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:17.403][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 23:31:17.404][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:17.405][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 23:31:17.408][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.412][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.413][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.414][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.415][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.418][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.420][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.421][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.424][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.425][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.428][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.430][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.430][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.431][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.433][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.434][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.436][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.451][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.454][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.461][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.465][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.465][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.466][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.467][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.467][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.471][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.473][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.476][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.479][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.482][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.483][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.488][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.489][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.492][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.495][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.498][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.501][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.504][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.505][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.508][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.509][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.510][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.510][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.511][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.514][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.517][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.520][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.521][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.524][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.525][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.526][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.527][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.530][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.533][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.536][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.536][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.540][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.541][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.542][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.543][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.546][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.549][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.552][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.553][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.558][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.559][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.562][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.565][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.568][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.568][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.576][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.580][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.581][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.583][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.587][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.590][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.591][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.592][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.593][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.594][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.594][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.597][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.599][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.600][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.603][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.606][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.607][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.609][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.609][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.610][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.613][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.615][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.620][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.622][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.625][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.626][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.630][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.630][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.631][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.632][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.633][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.638][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.641][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.642][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.642][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.646][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.647][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.648][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.651][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.654][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.658][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.661][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.663][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.667][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.673][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.673][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.674][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.677][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.679][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.679][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.686][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.689][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.689][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.690][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.694][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.696][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.698][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.711][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.712][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.717][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.724][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.725][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.728][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.729][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.729][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.733][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.738][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.741][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.744][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.749][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.750][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.751][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.757][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.760][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:17.761][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:17.761][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:17.765][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:17.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:17.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:17.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:17.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.770][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.773][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:17.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.786][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.789][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:17.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:17.820][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:17.822][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:17.823][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:17.825][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:18.229][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:18.640][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:18.642][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2024-11-19 23:31:18.646][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2024-11-19 23:31:18.648][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:18.651][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:18.652][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:18.653][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:19.060][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:19.459][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:19.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2024-11-19 23:31:19.466][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2024-11-19 23:31:19.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:19.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:19.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:19.475][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:19.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:19.476][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:19.477][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:19.478][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2024-11-19 23:31:19.479][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:19.480][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2024-11-19 23:31:19.481][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:19.482][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:19.482][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:19.483][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:19.484][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:19.485][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:19.487][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:19.487][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:19.488][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:19.492][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:19.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:19.493][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:19.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:19.494][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2024-11-19 23:31:19.496][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:19.497][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:19.498][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2024-11-19 23:31:20.006][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2024-11-19 23:31:20.416][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:20.419][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2024-11-19 23:31:20.422][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2024-11-19 23:31:20.424][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2024-11-19 23:31:20.425][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:20.426][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:20.427][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:20.428][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:20.429][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:20.429][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:20.434][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:20.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:20.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:20.436][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:20.437][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.438][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.439][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.440][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.441][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.444][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:20.444][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:20.445][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.446][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.447][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:20.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:20.448][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.450][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:20.450][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:20.451][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.452][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.453][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:20.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:20.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.456][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:20.456][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:20.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.458][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.459][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:20.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:20.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.461][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:20.462][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:20.463][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.464][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.465][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:20.466][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:20.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.468][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:20.469][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:20.469][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.470][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.471][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:20.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:20.472][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.474][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:20.475][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:20.475][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.476][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.477][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:20.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:20.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.480][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.480][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.481][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.482][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.483][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.485][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:20.486][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:20.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.488][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:20.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:20.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.491][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:20.492][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:20.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.493][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.494][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:20.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:20.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.510][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:20.511][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:20.511][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.512][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.513][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:20.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:20.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.516][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:20.517][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:20.518][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.519][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:20.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:20.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.522][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.525][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:20.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:20.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.528][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.533][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:20.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:20.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:20.569][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2024-11-19 23:31:20.570][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.573][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.576][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:20.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:20.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:20.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:20.654][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:20.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:20.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:20.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:20.657][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:20.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:20.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:20.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:20.666][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:20.667][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:20.667][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:20.671][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:20.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:20.672][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:20.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:20.674][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2024-11-19 23:31:20.674][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:20.676][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2024-11-19 23:31:20.677][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:20.678][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:20.678][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:20.679][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:20.680][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:20.680][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:20.683][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:20.683][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:20.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:20.687][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:20.688][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:20.689][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:20.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:20.690][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2024-11-19 23:31:20.692][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:20.693][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:20.694][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2024-11-19 23:31:21.116][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2024-11-19 23:31:21.531][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:21.534][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2024-11-19 23:31:21.538][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2024-11-19 23:31:21.540][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2024-11-19 23:31:21.541][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:21.543][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:21.544][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:21.545][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.546][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.547][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.555][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.556][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.559][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.560][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.561][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.562][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.566][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:21.567][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:21.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.568][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.569][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:21.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:21.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.572][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:21.573][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:21.574][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.575][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.576][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:21.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:21.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.578][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:21.579][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:21.580][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.581][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.581][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:21.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:21.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.584][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:21.585][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:21.586][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.587][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.587][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:21.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:21.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.590][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:21.591][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:21.592][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.593][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.594][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:21.594][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:21.595][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.596][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.597][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:21.597][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:21.598][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.600][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.600][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.601][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.602][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.603][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.606][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:21.606][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:21.607][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.608][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.609][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:21.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:21.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.612][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:21.612][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:21.613][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.614][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.615][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:21.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:21.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.618][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:21.619][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:21.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.620][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.621][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:21.622][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:21.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.624][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:21.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:21.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.627][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:21.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:21.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:21.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:21.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.636][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.639][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.642][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:21.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:21.653][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.654][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.655][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2024-11-19 23:31:21.655][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.656][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.658][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.661][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.691][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:21.694][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:21.695][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 23:31:21.696][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:21.697][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 23:31:21.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.700][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.701][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.704][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.707][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.710][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.713][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.716][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.717][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.724][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.727][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.730][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.733][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.734][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.739][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.745][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.746][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.749][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.752][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.755][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.756][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.757][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.758][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.762][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.766][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.767][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.769][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.772][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.775][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.778][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.781][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.784][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.785][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.789][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.790][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.794][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.795][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.801][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.801][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.802][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.805][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.808][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.819][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.822][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.825][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.832][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.833][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.836][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.837][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.838][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.840][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.843][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.844][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.848][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.849][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.850][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.854][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.857][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.859][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.860][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.860][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.863][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.864][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.871][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.875][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.878][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.879][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.881][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.882][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.882][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.886][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.887][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.892][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.898][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.899][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.903][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.915][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.925][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.932][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.937][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.941][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.944][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.947][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.948][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.961][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.962][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.963][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.964][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.967][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.970][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.973][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.974][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.974][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.978][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.979][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.980][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.983][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.986][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:21.989][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:21.989][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:21.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:21.993][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:21.994][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:21.995][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:21.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:21.996][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:21.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:21.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:21.999][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.000][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.002][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.005][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.005][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.009][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.010][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.015][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.017][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.020][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.021][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.021][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.024][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.026][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.027][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.030][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.033][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.036][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.036][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.037][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.040][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.041][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.042][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.048][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.049][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.051][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.052][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.059][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.061][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.064][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.079][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:22.087][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:22.089][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2024-11-19 23:31:22.090][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:22.091][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2024-11-19 23:31:22.094][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.094][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.095][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.099][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.100][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.101][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.101][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.104][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.107][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.116][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.119][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.120][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.121][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.123][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.126][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.127][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.129][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.132][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.133][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.136][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.137][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.141][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.144][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.147][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.150][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.153][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.157][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.158][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.159][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.159][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.160][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.166][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.169][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.171][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.172][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.174][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.182][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.185][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.188][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.189][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.190][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.190][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.191][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.192][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.195][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.196][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.197][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.200][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.203][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.206][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.207][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.210][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.219][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.222][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.228][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.228][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.229][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.232][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.233][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.234][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.235][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.238][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.241][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.244][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.244][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.245][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.249][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.250][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.253][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.256][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.259][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.260][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.260][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.263][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.265][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.266][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.269][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.272][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.275][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.276][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.279][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.280][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.280][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.281][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.282][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.287][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.290][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.291][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.294][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.296][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.297][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.300][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.303][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.306][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.306][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.311][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.316][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.321][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.322][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.322][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.325][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.327][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.333][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.341][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.342][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.347][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.353][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.358][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.363][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.364][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.365][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.368][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.381][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.383][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.389][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.390][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.395][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.402][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.404][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.405][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.409][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.410][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.412][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.415][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.420][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.421][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.421][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.424][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.426][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.427][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.433][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.445][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:22.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:22.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:31:22.453][biodb::testThat]
biodb.INFO [2024-11-19 23:31:22.454][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-11-19 23:31:22.454][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:22.455][biodb::testThat]
biodb.TRACE[2024-11-19 23:31:22.457][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:31:22.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:31:22.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.460][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.463][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.472][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.475][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.475][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.480][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.480][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.484][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.486][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.486][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:22.489][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:22.491][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:22.492][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 23:31:22.493][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:22.494][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 23:31:22.496][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.497][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.497][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.500][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.502][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.503][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.506][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.509][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.512][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:22.514][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:22.515][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 23:31:22.516][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:22.517][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 23:31:22.519][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.519][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.520][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.523][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.525][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.526][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.529][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.532][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.536][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.539][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.540][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.541][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.542][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.544][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.547][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:22.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.550][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 23:31:22.551][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.552][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.556][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.556][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.557][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.558][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.561][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.564][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.565][private$selectFields]
biodb.TRACE[2024-11-19 23:31:22.565][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:22.566][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:22.567][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.567][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.568][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.569][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.570][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.571][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.572][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.572][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.573][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.574][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.574][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.575][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.576][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.576][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.577][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:22.578][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.580][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.583][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.600][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-19 23:31:22.600][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.601][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.605][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.607][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.608][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.611][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.614][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.615][private$selectFields]
biodb.TRACE[2024-11-19 23:31:22.615][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:22.616][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:22.617][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.617][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.618][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.619][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.620][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.620][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.621][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.622][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.622][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.623][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.624][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.624][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.625][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.626][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.626][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.627][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:22.628][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.631][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.636][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 23:31:22.637][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.638][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.638][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.642][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.643][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:22.644][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.647][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.650][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.651][private$selectFields]
biodb.TRACE[2024-11-19 23:31:22.651][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:22.652][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:22.653][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.653][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.654][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.655][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.655][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.656][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.657][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.657][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.658][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.659][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.660][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:22.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.661][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.662][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.662][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.663][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:22.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.666][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.669][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:22.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.672][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-19 23:31:22.673][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 23:31:22.674][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 23:31:22.680][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.686][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.687][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:22.689][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:22.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:22.738][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:22.739][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:22.739][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:22.743][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:22.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:22.744][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:22.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:22.747][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:22.750][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:22.751][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:22.752][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:23.154][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:23.554][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:23.556][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2024-11-19 23:31:23.559][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2024-11-19 23:31:23.562][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:23.564][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:23.565][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:23.566][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:23.966][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:24.367][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:24.369][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2024-11-19 23:31:24.372][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2024-11-19 23:31:24.374][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.374][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.379][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.380][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.382][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.388][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.388][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.391][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.395][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.397][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.398][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.401][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.404][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.405][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.407][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.408][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.411][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.413][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.414][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.417][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.422][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.454][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 23:31:24.472][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.472][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.473][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.477][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.477][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.478][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.480][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.482][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.486][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.487][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.488][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.488][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.489][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.490][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.491][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.491][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.492][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.493][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.493][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.494][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.495][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.495][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.496][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.497][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.497][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.498][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.499][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.500][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.500][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.503][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.506][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.507][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.508][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.509][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-19 23:31:24.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.510][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.511][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.514][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.516][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.529][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.547][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.548][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.548][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.549][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.550][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.550][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.551][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.552][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.553][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.554][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.554][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.555][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.556][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.571][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.572][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.573][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.573][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.574][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.575][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.576][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.579][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.579][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.581][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.584][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 23:31:24.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.586][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.586][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.590][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.591][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.593][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.596][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.598][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.599][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.600][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.600][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.601][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.602][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.603][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.603][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.604][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.605][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.605][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.606][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.607][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.607][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.608][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.609][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.610][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.610][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.611][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.612][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.612][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.614][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.615][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.618][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.619][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.621][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-19 23:31:24.622][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 23:31:24.622][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 23:31:24.628][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:24.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:24.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:31:24.633][biodb::testThat]
biodb.INFO [2024-11-19 23:31:24.634][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-11-19 23:31:24.635][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:24.635][biodb::testThat]
biodb.TRACE[2024-11-19 23:31:24.638][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:31:24.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:31:24.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.641][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.644][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.646][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.649][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.654][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.655][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.655][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.659][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.659][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.660][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.661][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:24.663][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:24.665][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:24.666][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 23:31:24.667][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:24.668][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 23:31:24.670][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.670][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.675][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.676][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.677][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.680][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.683][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.693][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:24.695][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:24.696][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 23:31:24.697][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:24.698][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 23:31:24.700][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.701][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.702][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.706][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.706][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.708][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.711][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.714][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.717][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.717][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.721][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.722][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.724][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.727][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.729][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:24.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.732][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 23:31:24.733][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.734][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.735][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.738][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.739][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.747][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.750][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.753][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.753][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.754][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.755][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.755][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.756][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.757][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.757][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.758][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.759][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.760][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.761][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.762][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.762][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.763][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.764][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.764][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.765][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.766][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.766][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.769][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.772][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.775][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-19 23:31:24.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.780][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.783][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.786][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.789][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.790][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.790][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.791][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.792][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.792][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.793][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.794][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.794][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.795][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.796][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.797][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.797][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.798][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.799][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.799][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.800][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.801][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.801][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.802][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.803][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.804][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.806][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.819][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 23:31:24.820][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.820][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.821][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.830][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.831][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.832][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.834][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.834][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.835][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.836][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.836][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.837][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.838][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.838][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.839][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.840][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.841][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.842][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.843][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.843][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.844][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.845][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.846][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.847][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.847][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.850][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.853][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.856][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-19 23:31:24.857][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 23:31:24.857][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 23:31:24.863][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.866][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.869][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.872][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.876][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.877][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.881][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.882][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.882][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.883][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:24.885][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:24.887][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:24.888][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-19 23:31:24.889][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:24.890][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-19 23:31:24.892][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:24.895][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:24.896][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-19 23:31:24.896][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:24.897][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-19 23:31:24.899][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.900][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.904][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.905][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.906][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.909][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.912][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.916][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.919][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.921][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.922][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.923][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.924][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.925][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.928][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.931][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.931][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.932][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.935][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.936][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.938][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.946][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.947][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.950][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.951][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:24.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:24.953][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 23:31:24.955][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.955][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.956][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.961][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.961][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.965][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.968][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.969][private$selectFields]
biodb.TRACE[2024-11-19 23:31:24.969][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:24.970][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:24.971][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.971][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.972][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.973][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.973][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.974][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.975][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.975][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.976][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.977][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.977][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:24.978][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.979][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.980][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.980][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.981][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:24.982][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.985][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.987][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.988][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:24.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:24.990][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-19 23:31:24.991][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:24.992][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:24.992][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:24.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:24.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:24.997][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:24.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:24.998][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:24.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.004][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.005][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.005][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.006][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.006][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.007][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.008][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.009][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.009][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.010][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.011][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.011][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.012][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.013][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.013][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.014][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.015][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.015][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.016][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.017][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.018][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.022][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.023][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.026][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 23:31:25.027][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.028][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.031][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.033][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.034][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.037][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.040][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.041][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.041][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.042][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.043][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.043][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.044][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.045][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.045][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.046][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.047][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.048][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.049][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.049][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.050][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.051][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.052][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.053][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.054][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.056][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.059][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.062][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-19 23:31:25.068][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 23:31:25.069][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 23:31:25.076][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:25.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:25.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:31:25.082][biodb::testThat]
biodb.INFO [2024-11-19 23:31:25.082][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-11-19 23:31:25.083][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:25.084][biodb::testThat]
biodb.TRACE[2024-11-19 23:31:25.086][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-11-19 23:31:25.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-11-19 23:31:25.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.089][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.092][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.095][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.098][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.103][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.104][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.108][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.109][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:25.112][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:25.114][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:25.115][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2024-11-19 23:31:25.116][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:25.117][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2024-11-19 23:31:25.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.120][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.120][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.123][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.124][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.125][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.125][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.126][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.127][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.128][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.129][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.132][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.135][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:25.137][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:25.138][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2024-11-19 23:31:25.139][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:25.140][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2024-11-19 23:31:25.142][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.142][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.143][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.147][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.149][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.150][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.152][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.155][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.157][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.158][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.163][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.165][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.167][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.170][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:25.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.173][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 23:31:25.174][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.175][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.179][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.180][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.182][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.187][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.188][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.188][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.189][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.190][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.190][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.191][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.198][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.199][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.200][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.201][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.202][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.203][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.203][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.204][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.205][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.206][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.207][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.208][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.209][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.212][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.216][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.217][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.218][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [192288].
biodb.DEBUG[2024-11-19 23:31:25.218][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.219][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.220][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.223][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.224][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.225][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.226][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.228][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.231][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.232][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.233][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.233][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.234][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.235][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.235][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.236][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.237][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.238][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.238][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.239][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.240][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.240][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.241][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.242][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.242][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.243][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.244][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.244][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.245][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.248][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.251][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.252][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.253][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.254][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 23:31:25.255][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.255][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.259][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.260][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.265][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.267][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.268][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.269][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.269][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.270][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.271][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.271][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.273][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.273][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.274][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.276][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.276][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.277][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.278][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.278][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.279][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.280][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.280][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.281][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.284][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.287][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.287][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.290][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [209892].
biodb.DEBUG[2024-11-19 23:31:25.290][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 23:31:25.291][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 23:31:25.304][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.307][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.310][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.313][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.324][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.325][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.329][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.330][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.331][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:25.333][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:25.336][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:25.337][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2024-11-19 23:31:25.338][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:25.339][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2024-11-19 23:31:25.341][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:25.344][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:25.344][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2024-11-19 23:31:25.345][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:25.346][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2024-11-19 23:31:25.348][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.349][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.353][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.354][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.358][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.364][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.364][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.369][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.370][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.371][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.374][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.376][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.377][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.379][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.380][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.384][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.385][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.386][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.392][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:25.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:25.395][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-11-19 23:31:25.396][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.397][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.400][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.402][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.403][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.404][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.409][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.409][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.410][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.411][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.411][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.412][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.413][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.413][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.414][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.416][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.417][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.418][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.418][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.419][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.420][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.420][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.421][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.422][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.422][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.428][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.430][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.431][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2024-11-19 23:31:25.432][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.433][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.433][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.436][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.437][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.438][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.438][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.TRACE[2024-11-19 23:31:25.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.442][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.452][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.453][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.453][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.454][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.455][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.455][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.456][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.457][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.458][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.458][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.459][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.460][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.460][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.461][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.462][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.463][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.464][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.465][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.466][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.466][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.475][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2024-11-19 23:31:25.475][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.480][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.481][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:25.483][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.485][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.488][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.489][private$selectFields]
biodb.TRACE[2024-11-19 23:31:25.490][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-11-19 23:31:25.490][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-11-19 23:31:25.491][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.492][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.492][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.493][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.494][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.494][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.495][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.497][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.498][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2024-11-19 23:31:25.498][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.499][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.500][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.500][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.501][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2024-11-19 23:31:25.502][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.505][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.506][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.507][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.508][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:25.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:25.511][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2024-11-19 23:31:25.511][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-11-19 23:31:25.512][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-11-19 23:31:25.525][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:25.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-11-19 23:31:25.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:25.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-11-19 23:31:25.530][biodb::testThat]
biodb.INFO [2024-11-19 23:31:25.531][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-11-19 23:31:25.531][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:25.532][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:25.533][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-11-19 23:31:25.534][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:25.535][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-11-19 23:31:25.536][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:25.537][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:25.538][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:25.539][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:25.539][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:25.540][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:25.542][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:25.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:25.543][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:25.546][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:25.547][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:25.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:25.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:25.549][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2024-11-19 23:31:25.551][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:25.552][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:25.553][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2024-11-19 23:31:25.967][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2024-11-19 23:31:26.377][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:26.379][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2024-11-19 23:31:26.382][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2024-11-19 23:31:26.384][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2024-11-19 23:31:26.385][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:26.386][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:26.387][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:26.388][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:26.389][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:26.389][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:26.403][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:26.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:26.405][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:26.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:26.408][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.409][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.411][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.411][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.414][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:26.415][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:26.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.417][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.418][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:26.419][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:26.419][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.420][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.421][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:26.422][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:26.422][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.423][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.424][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:26.425][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:26.425][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.426][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.427][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:26.427][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:26.428][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.429][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.430][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:26.430][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:26.431][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.432][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.433][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:26.433][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:26.434][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.435][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.436][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:26.436][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:26.437][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.438][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.439][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:26.439][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:26.440][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.441][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.442][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:26.443][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:26.443][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.444][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.445][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:26.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:26.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.448][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:26.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:26.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.451][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:26.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:26.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.457][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.458][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.462][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.463][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.493][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.497][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:26.500][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:26.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:26.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:26.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:26.503][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2024-11-19 23:31:26.504][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-11-19 23:31:26.511][biodb::testThat]
biodb.INFO [2024-11-19 23:31:26.512][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-11-19 23:31:26.512][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:26.513][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:26.521][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2024-11-19 23:31:26.522][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2024-11-19 23:31:26.523][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2024-11-19 23:31:26.525][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2024-11-19 23:31:26.533][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2024-11-19 23:31:26.534][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:26.536][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:26.537][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:26.538][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:26.539][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:26.543][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:26.543][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:26.544][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:26.548][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:26.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:26.550][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:26.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:26.552][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2024-11-19 23:31:26.554][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:26.555][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:26.556][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2024-11-19 23:31:26.960][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2024-11-19 23:31:27.366][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:27.368][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2024-11-19 23:31:27.371][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2024-11-19 23:31:27.372][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:27.373][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:27.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:27.378][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:27.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:27.379][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:27.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:27.381][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2024-11-19 23:31:27.383][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:27.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:27.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2024-11-19 23:31:27.792][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2024-11-19 23:31:28.197][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:28.200][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2024-11-19 23:31:28.203][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2024-11-19 23:31:28.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:28.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:28.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:28.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:28.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:28.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:28.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:28.212][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2024-11-19 23:31:28.215][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:28.215][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:28.216][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2024-11-19 23:31:28.616][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2024-11-19 23:31:29.018][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:29.020][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2024-11-19 23:31:29.023][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2024-11-19 23:31:29.025][private$doSaveContentToFile] Saving to cache [3]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, /home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2024-11-19 23:31:29.026][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:29.027][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2024-11-19 23:31:29.028][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:29.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:29.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:29.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:29.035][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:29.035][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:29.036][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:29.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:29.038][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.039][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.040][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.041][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.044][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:29.045][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:29.046][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.046][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.047][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:29.048][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:29.049][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.049][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.050][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:29.051][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:29.052][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.053][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.053][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.054][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.055][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.056][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.056][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.057][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.058][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.059][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.059][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:29.060][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:29.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.062][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.062][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.063][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.064][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.065][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.065][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:29.066][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:29.067][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.068][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.069][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:29.069][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:29.070][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.071][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.072][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:29.072][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:29.073][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.074][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.077][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.079][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.080][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.083][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.100][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.104][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.108][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:29.110][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:29.111][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:29.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:29.115][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:29.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:29.117][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:29.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:29.119][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.120][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.121][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.121][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.122][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.125][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:29.126][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:29.126][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.127][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.128][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:29.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:29.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.131][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:29.132][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:29.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.133][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.134][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:29.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:29.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.137][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:29.138][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:29.138][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.139][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.140][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:29.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:29.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.144][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.144][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.145][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.146][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.149][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.149][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.150][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.151][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.152][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.154][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.155][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:29.155][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:29.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.157][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.157][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:29.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:29.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.160][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.161][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.162][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.162][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.163][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.166][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:29.167][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:29.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.168][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:29.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:29.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.172][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:29.173][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:29.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.174][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.175][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:29.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:29.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.178][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:29.179][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:29.180][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.180][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.181][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:29.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:29.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.184][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.187][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.188][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.190][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.193][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.196][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.198][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.201][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:29.204][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:29.205][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:29.205][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:29.209][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:29.210][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:29.211][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:29.211][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:29.213][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.214][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.216][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.216][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.219][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:29.220][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:29.227][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.228][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.229][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:29.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:29.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.232][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:29.233][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:29.234][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.235][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.236][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:29.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:29.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.239][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:29.239][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:29.240][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.241][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.242][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:29.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:29.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.245][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.245][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.246][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.247][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.248][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:29.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.250][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.251][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.252][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.252][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.253][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:29.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.256][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:29.257][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:29.258][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.258][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.259][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:29.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:29.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.262][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.263][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.264][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.265][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:29.266][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.267][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.268][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:29.269][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:29.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.270][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.271][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:29.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:29.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.274][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:29.275][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:29.275][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.276][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.277][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:29.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:29.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.280][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:29.281][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:29.281][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.282][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.283][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:29.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:29.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.286][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.288][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.294][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:29.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.307][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.308][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.309][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.311][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.314][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.317][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.322][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.325][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:29.328][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:29.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:29.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:29.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:29.331][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2024-11-19 23:31:29.332][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-11-19 23:31:29.332][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2024-11-19 23:31:29.342][biodb::testThat]
biodb.INFO [2024-11-19 23:31:29.342][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-11-19 23:31:29.343][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:29.344][biodb::testThat]
biodb.INFO [2024-11-19 23:31:29.368][biodb::testThat]
biodb.INFO [2024-11-19 23:31:29.369][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-11-19 23:31:29.370][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:29.370][biodb::testThat]
biodb.INFO [2024-11-19 23:31:29.376][biodb::testThat]
biodb.INFO [2024-11-19 23:31:29.376][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-11-19 23:31:29.377][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:29.378][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:29.380][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:29.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:29.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:29.384][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:29.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1%2A&searchCategory=CHEBI%20ID&maximumResults=100&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:30.459][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:30.461][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2024-11-19 23:31:30.465][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2024-11-19 23:31:30.475][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:30.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:30.476][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:30.477][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:30.478][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:30.478][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:30.479][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:30.480][ef$get] fields variable is a list.
biodb.INFO [2024-11-19 23:31:30.481][biodb::testThat]
biodb.INFO [2024-11-19 23:31:30.482][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-11-19 23:31:30.482][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:30.483][biodb::testThat]
biodb.ERROR[2024-11-19 23:31:30.493][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-11-19 23:31:30.505][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-11-19 23:31:30.514][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:31:30.515][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 23:31:30.516][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 23:31:30.517][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:31:30.517][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:30.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:30.519][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.520][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.521][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.INFO [2024-11-19 23:31:30.528][biodb::testContext]
biodb.INFO [2024-11-19 23:31:30.529][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:31:30.530][biodb::testContext] Test context - Test conversions
biodb.INFO [2024-11-19 23:31:30.530][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:31:30.531][biodb::testContext]
biodb.INFO [2024-11-19 23:31:30.532][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:31:30.534][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:31:30.537][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:30.537][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:31:30.538][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:31:30.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.541][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:31:30.541][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:31:30.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.543][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[2024-11-19 23:31:30.544][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:31:30.545][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:31:30.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.749][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:31:30.750][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:31:30.750][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:31:30.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.752][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[2024-11-19 23:31:30.753][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:31:30.754][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:31:30.755][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:31:30.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.757][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:31:30.758][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:31:30.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.760][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[2024-11-19 23:31:30.760][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:31:30.761][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:31:30.762][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:31:30.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.764][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:31:30.765][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:31:30.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.767][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:31:30.768][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:31:30.769][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:31:30.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.772][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:31:30.772][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:31:30.773][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:31:30.774][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:31:30.774][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:31:30.775][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:31:30.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.778][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:31:30.778][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:31:30.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.781][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:31:30.781][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:31:30.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.784][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:31:30.785][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:31:30.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.787][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:31:30.788][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:31:30.788][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.790][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:31:30.791][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:31:30.792][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.793][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.794][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:31:30.794][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:31:30.798][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:31:30.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.799][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.801][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:31:30.801][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:31:30.802][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:31:30.803][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.805][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:31:30.806][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.807][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 23:31:30.807][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.808][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:30.809][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.810][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.810][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.811][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.812][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:31:30.812][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:30.813][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.814][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:31:30.814][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:30.815][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.816][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.816][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:30.816][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:30.816][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:30.816][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:31:30.816][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:31:30.817][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:30.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.818][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.819][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:30.820][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.820][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.822][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.822][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:30.823][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:30.824][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.824][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.825][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:31:30.826][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.827][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:31:30.828][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.828][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:30.829][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.830][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.830][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.831][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.832][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:31:30.832][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:30.833][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.834][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:31:30.834][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:30.835][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.836][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.837][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:30.837][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:30.837][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:30.837][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:31:30.837][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:31:30.837][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:30.838][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.840][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:30.840][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.841][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.842][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.842][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.843][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:30.844][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:30.844][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.845][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.846][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:31:30.847][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.848][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 23:31:30.849][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.850][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:30.850][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.851][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.852][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.852][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.853][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:31:30.854][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:30.855][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.855][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:31:30.856][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:30.857][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.857][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.858][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.859][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:30.860][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.861][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:30.862][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.863][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.864][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.864][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:30.865][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:30.866][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.866][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.867][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:31:30.868][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.869][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:31:30.870][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.870][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:30.871][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.872][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.873][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.873][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.874][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:31:30.875][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:30.876][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.876][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:31:30.877][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:30.878][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.878][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:30.879][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.880][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:30.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.882][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.883][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:30.884][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:30.884][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:30.885][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:30.886][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.887][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:30.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:30.889][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:30.890][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:30.891][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:30.892][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.893][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.897][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[2024-11-19 23:31:30.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.901][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.903][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.905][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.906][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.907][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.912][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.913][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.916][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.917][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.918][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.921][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.923][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.924][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.925][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[2024-11-19 23:31:30.926][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.929][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.930][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.950][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.DEBUG[2024-11-19 23:31:30.951][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.957][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.958][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:30.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:30.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:30.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:30.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:30.963][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:31:30.965][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:31:30.966][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:31:30.967][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:31:30.969][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:31:30.970][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:31:30.971][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:31:30.973][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:31:30.974][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:31:30.975][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:31:30.976][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:31:30.978][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:31:30.979][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:31:30.980][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:31:30.982][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:31:30.983][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:31:30.984][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:31:30.986][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:31:30.987][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:31:30.988][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:31:30.989][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:31:30.991][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:31:30.997][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:31:30.998][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:31:30.999][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:31:31.000][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:31:31.001][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:31:31.002][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:31:31.003][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:31:31.004][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:31:31.005][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:31:31.006][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:31:31.007][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:31:31.008][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:31:31.009][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:31:31.010][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:31:31.011][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:31:31.012][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:31:31.013][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:31:31.014][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:31:31.015][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:31:31.016][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:31:31.017][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:31:31.018][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:31:31.019][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:31:31.020][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:31:31.020][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:31:31.021][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:31:31.022][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:31:31.023][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:31:31.024][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:31:31.025][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:31:31.026][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:31:31.027][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:31:31.028][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:31:31.029][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:31:31.030][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:31:31.031][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:31:31.032][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:31:31.033][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:31:31.034][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:31:31.035][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:31:31.036][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:31:31.037][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:31:31.038][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:31:31.039][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:31:31.040][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:31:31.041][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:31:31.042][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:31:31.043][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:31:31.044][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:31:31.045][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:31:31.046][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:31:31.047][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:31:31.048][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:31:31.049][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:31:31.050][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:31:31.051][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:31:31.052][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:31:31.053][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:31:31.054][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:31:31.054][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:31:31.055][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:31:31.057][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:31:31.058][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:31:31.059][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:31.059][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.060][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.062][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.063][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.063][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.065][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[2024-11-19 23:31:31.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.067][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.069][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.074][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.076][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.080][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.083][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.DEBUG[2024-11-19 23:31:31.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.085][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.088][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.089][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.092][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.DEBUG[2024-11-19 23:31:31.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.094][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.097][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.102][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.103][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.104][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[2024-11-19 23:31:31.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.106][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.111][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.112][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.116][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.122][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.123][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.125][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.126][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:31.126][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.128][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.129][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.130][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.DEBUG[2024-11-19 23:31:31.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:31.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:31.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:31.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:31.133][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:31.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:31.134][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.DEBUG[2024-11-19 23:31:31.136][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 23:31:31.137][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 23:31:31.138][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:31.139][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:31:31.140][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:31.141][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:31.141][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:31.142][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:31.143][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:31.143][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 23:31:31.144][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:31:31.145][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:31.146][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:31.146][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 23:31:31.147][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 23:31:31.148][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:31.149][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:31.149][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:31.149][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:31.150][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:31:31.151][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:31.151][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:31.152][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:31.153][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:31.153][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:31.154][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:31.155][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:31.155][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 23:31:31.155][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:31.156][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:31.156][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:31.157][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 23:31:31.157][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 23:31:31.158][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:31:31.159][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:31:31.160][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 23:31:31.161][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:31:31.163][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:31:31.164][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:31:31.166][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 23:31:31.167][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 23:31:31.168][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 23:31:31.169][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 23:31:31.170][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:31:31.171][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:31:31.171][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 23:31:31.172][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 23:31:31.173][biodb::testThat]
biodb.INFO [2024-11-19 23:31:31.174][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2024-11-19 23:31:31.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:31.175][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:31.178][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 23:31:31.181][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:31.182][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:31.183][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2024-11-19 23:31:31.579][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2024-11-19 23:31:32.092][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:32.098][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2024-11-19 23:31:32.105][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2024-11-19 23:31:32.108][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:32.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:32.111][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:32.117][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:32.524][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:32.927][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:32.930][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2024-11-19 23:31:32.933][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2024-11-19 23:31:32.935][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:32.936][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:32.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:32.941][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:32.941][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:32.942][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:32.943][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:32.944][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:32.959][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:32.959][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:32.961][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:33.365][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:33.768][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:33.771][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2024-11-19 23:31:33.774][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2024-11-19 23:31:33.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.777][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.782][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:33.795][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.795][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.796][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.799][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.800][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.801][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.801][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:33.805][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:33.807][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:33.808][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-19 23:31:33.809][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:33.810][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-19 23:31:33.811][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.812][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.813][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.816][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.817][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.817][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:33.819][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:33.821][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:33.822][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-19 23:31:33.823][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:33.824][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-19 23:31:33.826][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.826][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.827][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.830][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.831][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.831][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.832][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.DEBUG[2024-11-19 23:31:33.833][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.837][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.838][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.839][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[2024-11-19 23:31:33.842][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:33.844][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:33.845][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2024-11-19 23:31:33.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:33.846][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2024-11-19 23:31:33.848][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.848][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:33.855][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:33.857][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:33.858][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2024-11-19 23:31:33.859][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:33.860][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2024-11-19 23:31:33.862][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:33.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:33.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:33.866][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:33.867][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:33.868][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:33.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:33.869][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:33.872][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:33.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:33.874][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:34.275][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:34.677][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:34.679][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2024-11-19 23:31:34.683][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2024-11-19 23:31:34.685][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:34.685][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:34.686][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:34.690][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:34.691][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:34.691][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:34.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-19 23:31:34.696][biodb::testThat]
biodb.INFO [2024-11-19 23:31:34.697][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2024-11-19 23:31:34.698][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:34.698][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:34.701][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI=1S/C15H24/c1-9(2)11-7-8-15(4)12-6-5-10(3)14(15)13(11)12/h5,9,11-14H,6-8H2,1-4H3/t11?,12?,13?,14?,15-/m0/s1&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:34.704][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:34.704][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:34.706][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:35.108][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:35.512][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:35.514][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2024-11-19 23:31:35.518][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2024-11-19 23:31:35.520][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:35.521][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:35.522][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:35.526][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:35.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:35.527][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:35.528][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:35.531][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:35.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:35.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:35.536][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:35.944][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:36.352][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:36.354][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2024-11-19 23:31:36.357][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2024-11-19 23:31:36.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:36.359][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.364][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.366][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.366][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.INFO [2024-11-19 23:31:36.370][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:31:36.371][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 23:31:36.372][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 23:31:36.372][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:31:36.373][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.373][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.374][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.375][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.375][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.376][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-19 23:31:36.379][biodb::testContext]
biodb.INFO [2024-11-19 23:31:36.380][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:31:36.380][biodb::testContext] Test context - Test web services
biodb.INFO [2024-11-19 23:31:36.381][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:31:36.382][biodb::testContext]
biodb.INFO [2024-11-19 23:31:36.383][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:31:36.385][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:31:36.388][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:36.388][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:31:36.389][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:31:36.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.392][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:31:36.392][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:31:36.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.394][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[2024-11-19 23:31:36.395][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:31:36.396][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:31:36.396][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.398][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:31:36.399][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:31:36.400][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:31:36.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.402][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[2024-11-19 23:31:36.403][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:31:36.403][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:31:36.404][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:31:36.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.407][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:31:36.408][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:31:36.408][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.410][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[2024-11-19 23:31:36.410][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:31:36.411][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:31:36.412][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:31:36.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.414][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.418][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:31:36.419][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:31:36.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.421][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.422][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:31:36.423][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:31:36.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:31:36.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.450][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.451][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:31:36.451][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:31:36.452][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:31:36.453][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:31:36.453][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:31:36.454][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:31:36.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.456][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.457][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:31:36.457][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:31:36.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.460][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:31:36.461][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:31:36.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.463][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:31:36.464][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:31:36.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.466][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:31:36.467][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:31:36.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.469][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[2024-11-19 23:31:36.470][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:31:36.470][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:31:36.471][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.473][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:31:36.474][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:31:36.477][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:31:36.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.480][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:31:36.480][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:31:36.481][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:31:36.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.484][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:31:36.485][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.486][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 23:31:36.487][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.488][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:36.488][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.489][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.490][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.490][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.491][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:31:36.492][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:36.493][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.493][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:31:36.494][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:36.495][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.495][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.496][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:36.496][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:36.496][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:36.496][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:31:36.496][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:31:36.497][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:36.497][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.498][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.499][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:36.499][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.500][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.501][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.501][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.502][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:36.503][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:36.503][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.504][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.505][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:31:36.506][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.507][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:31:36.508][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.508][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:36.509][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.510][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.510][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.511][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.512][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:31:36.512][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:36.513][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.514][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:31:36.514][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:36.515][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.516][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.517][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:36.517][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:36.517][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:36.517][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:31:36.517][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:31:36.517][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:36.518][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.519][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.519][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:36.520][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.521][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.521][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.522][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.523][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:36.523][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:36.524][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.525][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.525][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:31:36.527][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.527][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 23:31:36.528][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.529][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:36.529][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.530][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.531][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.531][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.532][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:31:36.533][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:36.534][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.534][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:31:36.535][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:36.536][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.536][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.537][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.538][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:36.539][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.539][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.540][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:36.541][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.541][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.542][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.543][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.543][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:36.544][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:36.545][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.546][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.546][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:31:36.548][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.548][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:31:36.549][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.550][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:36.551][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.551][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.552][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.553][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.553][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:31:36.554][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:36.555][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.556][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:31:36.556][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:36.557][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.558][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.558][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.559][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:36.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.560][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.561][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:36.562][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.563][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.564][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.564][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:36.565][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:36.565][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.566][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:36.567][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:36.568][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.568][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.569][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.570][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.572][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.572][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.573][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.573][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.574][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.575][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.576][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.578][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.578][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.580][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.581][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.581][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.583][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.584][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[2024-11-19 23:31:36.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.591][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.595][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.596][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.601][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.602][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.603][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.616][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.617][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.620][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.623][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:31:36.624][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:31:36.625][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:31:36.626][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:31:36.627][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:31:36.628][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:31:36.629][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:31:36.630][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:31:36.630][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:31:36.631][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:31:36.632][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:31:36.633][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:31:36.634][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:31:36.635][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:31:36.636][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:31:36.637][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:31:36.638][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:31:36.639][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:31:36.640][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:31:36.641][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:31:36.642][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:31:36.643][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:31:36.644][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:31:36.645][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:31:36.646][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:31:36.647][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:31:36.648][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:31:36.649][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:31:36.650][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:31:36.651][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:31:36.652][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:31:36.653][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:31:36.654][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:31:36.655][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:31:36.656][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:31:36.657][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:31:36.658][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:31:36.659][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:31:36.660][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:31:36.666][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:31:36.667][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:31:36.668][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:31:36.669][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:31:36.670][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:31:36.671][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:31:36.672][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:31:36.673][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:31:36.674][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:31:36.675][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:31:36.676][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:31:36.677][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:31:36.678][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:31:36.679][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:31:36.680][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:31:36.681][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:31:36.682][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:31:36.683][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:31:36.684][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:31:36.685][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:31:36.686][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:31:36.687][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:31:36.688][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:31:36.689][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:31:36.690][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:31:36.691][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:31:36.692][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:31:36.693][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:31:36.694][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:31:36.695][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:31:36.696][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:31:36.697][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:31:36.698][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:31:36.699][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:31:36.700][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:31:36.701][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:31:36.702][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:31:36.703][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:31:36.704][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:31:36.705][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:31:36.706][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:31:36.707][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:31:36.708][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:31:36.709][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:31:36.710][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:31:36.711][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:31:36.712][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:36.713][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.713][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.714][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.716][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.718][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.718][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.719][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.720][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.721][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.722][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.723][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.723][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[2024-11-19 23:31:36.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.725][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.730][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.731][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.735][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.738][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.747][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.750][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.756][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.769][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.774][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.775][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.777][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.779][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.782][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.784][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:36.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:36.787][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:36.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:36.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:36.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:36.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:36.791][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 23:31:36.792][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 23:31:36.793][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.794][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.795][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:36.796][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.797][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.798][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.798][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 23:31:36.799][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:31:36.800][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:36.800][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.801][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 23:31:36.802][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 23:31:36.803][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:36.804][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:36.804][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:36.804][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:36.805][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:31:36.805][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.806][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.807][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:36.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:36.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:36.809][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:36.810][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:36.810][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 23:31:36.810][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:36.811][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:36.812][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:36.812][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 23:31:36.812][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 23:31:36.813][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:31:36.815][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:31:36.816][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 23:31:36.817][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:31:36.818][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:31:36.819][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:31:36.822][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 23:31:36.822][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 23:31:36.823][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 23:31:36.824][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 23:31:36.825][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:31:36.826][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:31:36.827][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 23:31:36.828][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 23:31:36.829][biodb::testThat]
biodb.INFO [2024-11-19 23:31:36.829][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2024-11-19 23:31:36.830][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:36.831][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:36.833][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 23:31:36.836][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:36.837][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 23:31:36.838][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:36.839][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 23:31:36.842][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:36.844][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:36.845][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:36.846][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2024-11-19 23:31:37.249][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2024-11-19 23:31:37.651][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:37.653][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2024-11-19 23:31:37.656][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2024-11-19 23:31:37.662][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:31:37.663][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 23:31:37.664][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 23:31:37.665][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:31:37.665][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:37.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:37.667][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.668][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-11-19 23:31:37.671][biodb::testContext]
biodb.INFO [2024-11-19 23:31:37.672][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:31:37.673][biodb::testContext] Test context - Non regression tests
biodb.INFO [2024-11-19 23:31:37.673][biodb::testContext] ********************************************************************************
biodb.INFO [2024-11-19 23:31:37.674][biodb::testContext]
biodb.INFO [2024-11-19 23:31:37.676][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:31:37.677][self$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2024-11-19 23:31:37.680][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:37.680][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-11-19 23:31:37.681][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-11-19 23:31:37.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.684][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-11-19 23:31:37.684][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-11-19 23:31:37.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.687][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-11-19 23:31:37.688][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-11-19 23:31:37.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.699][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-11-19 23:31:37.699][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-11-19 23:31:37.700][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-11-19 23:31:37.701][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.703][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-11-19 23:31:37.703][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-11-19 23:31:37.704][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-11-19 23:31:37.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.706][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.706][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-11-19 23:31:37.707][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-11-19 23:31:37.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.710][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-11-19 23:31:37.710][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-11-19 23:31:37.711][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-11-19 23:31:37.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.713][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[2024-11-19 23:31:37.714][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-11-19 23:31:37.714][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-11-19 23:31:37.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.717][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-11-19 23:31:37.717][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-11-19 23:31:37.718][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-11-19 23:31:37.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.721][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:31:37.721][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-11-19 23:31:37.722][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-11-19 23:31:37.723][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-11-19 23:31:37.723][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-11-19 23:31:37.724][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-11-19 23:31:37.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.726][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-11-19 23:31:37.727][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-11-19 23:31:37.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.729][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.730][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-11-19 23:31:37.730][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-11-19 23:31:37.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.732][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.733][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-11-19 23:31:37.734][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-11-19 23:31:37.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.735][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[2024-11-19 23:31:37.736][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-11-19 23:31:37.737][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-11-19 23:31:37.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.739][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-11-19 23:31:37.740][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-11-19 23:31:37.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.742][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[2024-11-19 23:31:37.742][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-11-19 23:31:37.743][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-11-19 23:31:37.747][self$set] Set key svn.binary.path to "/usr/bin/svn".
biodb.DEBUG[2024-11-19 23:31:37.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.748][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.749][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.750][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-11-19 23:31:37.750][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-11-19 23:31:37.751][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-11-19 23:31:37.752][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.753][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[2024-11-19 23:31:37.754][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-11-19 23:31:37.755][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.756][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-11-19 23:31:37.756][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.757][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:37.758][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.758][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.759][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.760][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.760][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:31:37.761][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:37.762][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.763][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-11-19 23:31:37.763][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:37.764][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.765][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.765][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:37.765][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:37.765][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:37.765][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:31:37.765][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:31:37.766][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:37.767][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.767][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.768][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:37.769][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.769][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.770][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.771][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.771][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:37.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:37.772][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.773][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.774][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-11-19 23:31:37.775][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.776][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:31:37.776][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.777][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:37.778][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.778][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.779][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.780][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.780][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:31:37.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:37.782][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.783][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-11-19 23:31:37.783][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:37.784][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.785][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.785][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:37.785][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:37.785][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:37.785][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-11-19 23:31:37.785][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-11-19 23:31:37.786][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:37.787][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:37.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.789][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.790][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.791][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.791][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:37.792][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:37.793][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.794][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.795][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-11-19 23:31:37.796][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.796][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-11-19 23:31:37.797][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.798][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:37.799][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.800][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.801][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.801][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-11-19 23:31:37.802][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:37.803][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.803][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-11-19 23:31:37.804][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:37.805][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.805][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.806][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:37.807][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.808][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.809][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:37.809][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.810][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.811][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.811][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.812][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:37.813][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:37.813][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.814][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.815][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-11-19 23:31:37.816][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.816][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-11-19 23:31:37.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:37.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.819][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.820][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.821][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.821][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-11-19 23:31:37.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:37.823][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.823][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-11-19 23:31:37.824][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:37.825][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.825][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:37.826][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.827][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-11-19 23:31:37.828][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.828][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.829][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:37.830][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:37.830][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:37.831][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:37.832][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.832][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:37.833][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:37.833][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:37.834][self$setPropertyValue]
biodb.DEBUG[2024-11-19 23:31:37.835][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:37.836][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.838][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.845][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.849][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.849][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.857][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.861][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.862][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.866][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.869][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.870][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.873][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.874][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.876][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.879][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.882][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.885][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.DEBUG[2024-11-19 23:31:37.886][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.887][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.888][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.889][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-11-19 23:31:37.890][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-11-19 23:31:37.891][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-11-19 23:31:37.892][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-11-19 23:31:37.893][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:31:37.894][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-11-19 23:31:37.895][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-11-19 23:31:37.896][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-11-19 23:31:37.897][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-11-19 23:31:37.898][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-11-19 23:31:37.899][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:31:37.900][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-11-19 23:31:37.901][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-11-19 23:31:37.902][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-11-19 23:31:37.903][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-11-19 23:31:37.904][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-11-19 23:31:37.905][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-11-19 23:31:37.911][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-11-19 23:31:37.912][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:31:37.913][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-11-19 23:31:37.914][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-11-19 23:31:37.915][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-11-19 23:31:37.916][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-11-19 23:31:37.917][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-11-19 23:31:37.918][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-11-19 23:31:37.919][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-11-19 23:31:37.920][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-11-19 23:31:37.921][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-11-19 23:31:37.922][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-11-19 23:31:37.923][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-11-19 23:31:37.924][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-11-19 23:31:37.925][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-11-19 23:31:37.925][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-11-19 23:31:37.926][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-11-19 23:31:37.927][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-11-19 23:31:37.928][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-11-19 23:31:37.929][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-11-19 23:31:37.930][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-11-19 23:31:37.931][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-11-19 23:31:37.932][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-11-19 23:31:37.933][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-11-19 23:31:37.934][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-11-19 23:31:37.935][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-11-19 23:31:37.936][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-11-19 23:31:37.937][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-11-19 23:31:37.938][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-11-19 23:31:37.939][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-11-19 23:31:37.940][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-11-19 23:31:37.941][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-11-19 23:31:37.942][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-11-19 23:31:37.943][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-11-19 23:31:37.944][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-11-19 23:31:37.945][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-11-19 23:31:37.946][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-11-19 23:31:37.947][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-11-19 23:31:37.948][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-11-19 23:31:37.948][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-11-19 23:31:37.949][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-11-19 23:31:37.950][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-11-19 23:31:37.951][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-11-19 23:31:37.952][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-11-19 23:31:37.953][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-11-19 23:31:37.954][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-11-19 23:31:37.955][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-11-19 23:31:37.956][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-11-19 23:31:37.957][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-11-19 23:31:37.958][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:31:37.959][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:31:37.960][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-11-19 23:31:37.961][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-11-19 23:31:37.962][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-11-19 23:31:37.963][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-11-19 23:31:37.964][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-11-19 23:31:37.965][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-11-19 23:31:37.966][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-11-19 23:31:37.967][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-11-19 23:31:37.968][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-11-19 23:31:37.969][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-11-19 23:31:37.969][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-11-19 23:31:37.970][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-11-19 23:31:37.971][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-11-19 23:31:37.972][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-11-19 23:31:37.973][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-11-19 23:31:37.974][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-11-19 23:31:37.976][initialize] This is biodb version 1.14.0.
biodb.DEBUG[2024-11-19 23:31:37.976][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-11-19 23:31:37.977][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.978][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.979][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:37.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:37.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.983][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.984][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:37.985][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:37.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.986][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:37.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:37.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:37.992][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:37.993][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:37.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:37.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:37.996][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.DEBUG[2024-11-19 23:31:37.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:37.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:37.998][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:37.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:37.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.001][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.002][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.005][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[2024-11-19 23:31:38.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.006][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.010][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.012][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.012][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.013][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[2024-11-19 23:31:38.014][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.015][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.016][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.019][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.028][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.031][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.032][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.038][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[2024-11-19 23:31:38.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.040][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.044][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.047][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-11-19 23:31:38.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.049][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.052][biodb$loadDefinitions] Load definitions from file "/media/volume/teran2_disk/biocbuild/bbs-3.20-bioc/R/site-library/biodbChebi/definitions.yml".
biodb.DEBUG[2024-11-19 23:31:38.053][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2024-11-19 23:31:38.055][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:38.056][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-11-19 23:31:38.056][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:38.057][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-11-19 23:31:38.058][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:38.059][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-11-19 23:31:38.059][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:38.060][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2024-11-19 23:31:38.061][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2024-11-19 23:31:38.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-11-19 23:31:38.062][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:38.063][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2024-11-19 23:31:38.063][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2024-11-19 23:31:38.064][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2024-11-19 23:31:38.065][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-11-19 23:31:38.066][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-11-19 23:31:38.066][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-11-19 23:31:38.066][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-11-19 23:31:38.066][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2024-11-19 23:31:38.067][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:38.068][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:38.068][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-11-19 23:31:38.069][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-11-19 23:31:38.070][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-11-19 23:31:38.070][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-11-19 23:31:38.071][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:38.071][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2024-11-19 23:31:38.072][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-11-19 23:31:38.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-11-19 23:31:38.073][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-11-19 23:31:38.074][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2024-11-19 23:31:38.074][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2024-11-19 23:31:38.075][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-11-19 23:31:38.076][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-11-19 23:31:38.077][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2024-11-19 23:31:38.078][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-11-19 23:31:38.079][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-11-19 23:31:38.080][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-11-19 23:31:38.082][super$initialize] Initialize connector chebi.
biodb.DEBUG[2024-11-19 23:31:38.083][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2024-11-19 23:31:38.084][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2024-11-19 23:31:38.085][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2024-11-19 23:31:38.086][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:31:38.087][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2024-11-19 23:31:38.088][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2024-11-19 23:31:38.088][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2024-11-19 23:31:38.090][biodb::testThat]
biodb.INFO [2024-11-19 23:31:38.090][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2024-11-19 23:31:38.091][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-11-19 23:31:38.092][biodb::testThat]
biodb.DEBUG[2024-11-19 23:31:38.094][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2024-11-19 23:31:38.097][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:38.098][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2024-11-19 23:31:38.099][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:38.100][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2024-11-19 23:31:38.102][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2024-11-19 23:31:38.105][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-11-19 23:31:38.106][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2024-11-19 23:31:38.106][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-11-19 23:31:38.107][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2024-11-19 23:31:38.111][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2024-11-19 23:31:38.112][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2024-11-19 23:31:38.113][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2024-11-19 23:31:38.114][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-11-19 23:31:38.114][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-11-19 23:31:38.115][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2024-11-19 23:31:38.116][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2024-11-19 23:31:38.117][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-11-19 23:31:38.117][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-11-19 23:31:38.119][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:38.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:38.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:38.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:38.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:38.130][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:38.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-11-19 23:31:38.132][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2024-11-19 23:31:38.134][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-11-19 23:31:38.134][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-11-19 23:31:38.135][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2024-11-19 23:31:38.542][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2024-11-19 23:31:39.436][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-11-19 23:31:39.438][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2024-11-19 23:31:39.440][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2024-11-19 23:31:39.442][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2024-11-19 23:31:39.443][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-11-19 23:31:39.444][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2024-11-19 23:31:39.445][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2024-11-19 23:31:39.447][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-11-19 23:31:39.447][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:39.448][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:39.452][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:39.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:39.453][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:39.454][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-11-19 23:31:39.456][ef$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.457][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.458][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.458][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.471][ef$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:39.471][ef$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:39.472][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.473][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.474][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2024-11-19 23:31:39.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2024-11-19 23:31:39.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.477][ef$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:39.477][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:39.478][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.479][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.480][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-11-19 23:31:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-11-19 23:31:39.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.482][ef$get] Asked field names are: inchi.
biodb.TRACE[2024-11-19 23:31:39.483][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2024-11-19 23:31:39.484][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.485][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.485][ef$get] Asked field names are: inchikey.
biodb.TRACE[2024-11-19 23:31:39.486][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2024-11-19 23:31:39.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.488][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.489][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:39.489][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:39.490][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.491][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.491][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:39.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-11-19 23:31:39.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.494][ef$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:39.495][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:39.496][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.496][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.497][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2024-11-19 23:31:39.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-11-19 23:31:39.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.500][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:39.501][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:39.501][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.502][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:39.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-11-19 23:31:39.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.505][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.506][ef$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:39.506][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:39.507][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.508][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.509][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-11-19 23:31:39.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-11-19 23:31:39.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.511][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.512][ef$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:39.513][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:39.513][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.514][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.515][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2024-11-19 23:31:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2024-11-19 23:31:39.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.518][ef$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:39.518][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:39.519][ef$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.520][ef$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.521][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2024-11-19 23:31:39.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2024-11-19 23:31:39.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.524][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:39.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:39.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.527][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:39.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:39.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.532][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-11-19 23:31:39.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-11-19 23:31:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.534][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.538][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.543][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.545][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.546][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.547][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-11-19 23:31:39.549][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-11-19 23:31:39.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-11-19 23:31:39.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-11-19 23:31:39.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-11-19 23:31:39.552][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2024-11-19 23:31:39.555][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-11-19 23:31:39.556][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2024-11-19 23:31:39.556][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2024-11-19 23:31:39.557][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-11-19 23:31:39.558][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-11-19 23:31:39.558][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-11-19 23:31:39.559][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-11-19 23:31:39.559][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-11-19 23:31:39.560][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-11-19 23:31:39.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 386 ]
>
> proc.time()
user system elapsed
15.504 0.839 55.484
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 1.236 | 0.070 | 2.360 | |
| ChebiEntry | 0.101 | 0.004 | 0.104 | |