Pierrick Roger
| Snapshot Date: 2025-08-14 13:40 -0400 (Thu, 14 Aug 2025) |
| git_url: https://git.bioconductor.org/packages/biodbChebi |
| git_branch: RELEASE_3_21 |
| git_last_commit: b8d718f |
| git_last_commit_date: 2025-04-15 12:39:10 -0400 (Tue, 15 Apr 2025) |
| Back to Multiple platform build/check report for BioC 3.21: simplified long |
|
This page was generated on 2025-08-18 11:41 -0400 (Mon, 18 Aug 2025).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4824 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.5.1 (2025-06-13 ucrt) -- "Great Square Root" | 4566 |
| merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4604 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4545 |
| kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4579 |
| 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 206/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbChebi 1.14.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | OK | | ||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | OK | OK | | ||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | OK | OK | | ||||||||
| kunpeng2 | Linux (openEuler 24.03 LTS) / 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: 1.14.0 |
| Command: E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbChebi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings biodbChebi_1.14.0.tar.gz |
| StartedAt: 2025-08-14 23:53:32 -0400 (Thu, 14 Aug 2025) |
| EndedAt: 2025-08-15 00:03:31 -0400 (Fri, 15 Aug 2025) |
| EllapsedTime: 598.4 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbChebi.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbChebi.install-out.txt --library=E:\biocbuild\bbs-3.21-bioc\R\library --no-vignettes --timings biodbChebi_1.14.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'E:/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck'
* using R version 4.5.1 (2025-06-13 ucrt)
* using platform: x86_64-w64-mingw32
* R was compiled by
gcc.exe (GCC) 14.2.0
GNU Fortran (GCC) 14.2.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbChebi/DESCRIPTION' ... OK
* this is package 'biodbChebi' version '1.14.0'
* 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 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 dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
ChebiConn 3.56 2.54 176.92
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
3. └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
id.col %in% colnames(ret) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id.col %in% colnames(ret))
[ FAIL 22 | WARN 0 | SKIP 0 | PASS 210 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
'E:/biocbuild/bbs-3.21-bioc/meat/biodbChebi.Rcheck/00check.log'
for details.
biodbChebi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### E:\biocbuild\bbs-3.21-bioc\R\bin\R.exe CMD INSTALL biodbChebi ### ############################################################################## ############################################################################## * installing to library 'E:/biocbuild/bbs-3.21-bioc/R/library' * installing *source* package 'biodbChebi' ... ** this is package 'biodbChebi' version '1.14.0' ** 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.fail
R version 4.5.1 (2025-06-13 ucrt) -- "Great Square Root"
Copyright (C) 2025 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64
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 [2025-08-15 00:02:05.515][biodb::testContext]
biodb.INFO [2025-08-15 00:02:05.519][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:02:05.520][biodb::testContext] Test context - Generic tests
biodb.INFO [2025-08-15 00:02:05.521][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:02:05.523][biodb::testContext]
biodb.INFO [2025-08-15 00:02:05.531][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:02:05.534][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-15 00:02:05.556][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:02:05.558][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-15 00:02:05.559][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-15 00:02:05.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.561][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.562][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.564][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-15 00:02:05.580][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-15 00:02:05.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.584][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[2025-08-15 00:02:05.585][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-15 00:02:05.587][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-15 00:02:05.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.591][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-15 00:02:05.593][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-15 00:02:05.594][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-15 00:02:05.595][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.596][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.598][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-15 00:02:05.600][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-15 00:02:05.601][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-15 00:02:05.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.608][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-15 00:02:05.610][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-15 00:02:05.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.615][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-15 00:02:05.616][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-15 00:02:05.617][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-15 00:02:05.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.622][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-15 00:02:05.623][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-15 00:02:05.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.628][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-15 00:02:05.629][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-15 00:02:05.630][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-15 00:02:05.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.634][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.635][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:02:05.636][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-15 00:02:05.638][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-15 00:02:05.639][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-15 00:02:05.640][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-15 00:02:05.641][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-15 00:02:05.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.645][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.646][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-15 00:02:05.647][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-15 00:02:05.648][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.650][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.652][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-15 00:02:05.653][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-15 00:02:05.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.656][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.657][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-15 00:02:05.659][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-15 00:02:05.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.662][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.663][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-15 00:02:05.664][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-15 00:02:05.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.669][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-15 00:02:05.670][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-15 00:02:05.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.673][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.675][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:02:05.676][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-15 00:02:05.679][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-15 00:02:05.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.683][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[2025-08-15 00:02:05.684][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-15 00:02:05.685][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-15 00:02:05.687][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-15 00:02:05.688][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.689][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.690][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.693][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-15 00:02:05.722][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.737][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-15 00:02:05.744][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.746][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:05.747][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.748][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.749][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.750][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.752][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:02:05.753][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:05.754][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.755][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-15 00:02:05.757][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:05.758][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.759][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.760][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:02:05.760][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:02:05.760][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:02:05.760][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:02:05.760][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:02:05.762][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:05.763][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.764][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.765][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:05.766][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.768][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.769][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.770][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.771][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:05.772][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:05.774][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.775][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.776][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-15 00:02:05.778][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.779][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:02:05.781][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.782][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:05.783][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.784][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.786][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.787][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.788][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:02:05.789][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:05.791][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.792][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-15 00:02:05.793][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:05.794][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.796][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.797][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:02:05.797][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:02:05.797][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:02:05.797][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:02:05.797][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:02:05.798][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:05.799][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:05.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.804][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.805][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.807][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:05.809][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:05.810][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.811][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.813][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-15 00:02:05.815][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.816][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-15 00:02:05.817][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.818][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:05.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.822][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.823][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.824][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:02:05.826][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:05.827][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.828][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-15 00:02:05.829][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:05.831][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.832][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.833][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.834][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:05.835][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.837][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.838][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:05.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.841][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.843][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.844][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:05.845][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:05.846][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.847][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.849][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-15 00:02:05.851][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.852][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:02:05.853][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.854][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:05.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.857][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.858][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.859][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.860][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:02:05.862][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:05.863][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.864][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-15 00:02:05.865][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:05.867][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.868][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:05.869][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.870][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:05.872][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.873][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.874][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:05.875][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:05.876][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:05.877][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:05.879][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.880][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:05.881][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:05.882][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:05.884][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:05.887][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:02:05.888][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.890][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.891][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.892][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.893][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.895][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.899][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.901][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[2025-08-15 00:02:05.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.904][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.906][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[2025-08-15 00:02:05.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.910][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.912][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.913][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.915][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.918][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.919][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.921][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.923][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[2025-08-15 00:02:05.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.927][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.928][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.929][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.930][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.931][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.936][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.940][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[2025-08-15 00:02:05.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.943][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.946][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[2025-08-15 00:02:05.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.948][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.953][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.963][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.DEBUG[2025-08-15 00:02:05.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.979][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[2025-08-15 00:02:05.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:05.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:05.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:05.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:05.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:05.992][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-15 00:02:05.996][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-15 00:02:05.998][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-15 00:02:06.000][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-15 00:02:06.001][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:02:06.003][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-15 00:02:06.005][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-15 00:02:06.006][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-15 00:02:06.008][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-15 00:02:06.009][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-15 00:02:06.011][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:02:06.013][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-15 00:02:06.014][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-15 00:02:06.016][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-15 00:02:06.017][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-15 00:02:06.019][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-15 00:02:06.021][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-15 00:02:06.022][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-15 00:02:06.024][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:02:06.025][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-15 00:02:06.027][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-15 00:02:06.029][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-15 00:02:06.030][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-15 00:02:06.032][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-15 00:02:06.033][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-15 00:02:06.035][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-15 00:02:06.037][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-15 00:02:06.038][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-15 00:02:06.040][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-15 00:02:06.041][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-15 00:02:06.043][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-15 00:02:06.045][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-15 00:02:06.046][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-15 00:02:06.048][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-15 00:02:06.049][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-15 00:02:06.051][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-15 00:02:06.053][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-15 00:02:06.054][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-15 00:02:06.056][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-15 00:02:06.059][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-15 00:02:06.060][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-15 00:02:06.062][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-15 00:02:06.064][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-15 00:02:06.065][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-15 00:02:06.067][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-15 00:02:06.069][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-15 00:02:06.070][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-15 00:02:06.072][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-15 00:02:06.074][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-15 00:02:06.075][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-15 00:02:06.077][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-15 00:02:06.079][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-15 00:02:06.080][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-15 00:02:06.082][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-15 00:02:06.083][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-15 00:02:06.085][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-15 00:02:06.087][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-15 00:02:06.088][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-15 00:02:06.090][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-15 00:02:06.092][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-15 00:02:06.093][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-15 00:02:06.095][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-15 00:02:06.096][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-15 00:02:06.098][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-15 00:02:06.100][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-15 00:02:06.101][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-15 00:02:06.103][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:02:06.105][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:02:06.106][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-15 00:02:06.108][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-15 00:02:06.110][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-15 00:02:06.111][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-15 00:02:06.113][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-15 00:02:06.114][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-15 00:02:06.116][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-15 00:02:06.118][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-15 00:02:06.119][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-15 00:02:06.121][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-15 00:02:06.122][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-15 00:02:06.124][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-15 00:02:06.126][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-15 00:02:06.127][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-15 00:02:06.129][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-15 00:02:06.153][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-15 00:02:06.156][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:02:06.159][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:02:06.160][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.162][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.163][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.164][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.DEBUG[2025-08-15 00:02:06.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.178][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.189][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[2025-08-15 00:02:06.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.197][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.DEBUG[2025-08-15 00:02:06.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.203][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.205][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[2025-08-15 00:02:06.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.211][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.213][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.215][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.216][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.227][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.230][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.232][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.234][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.238][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.240][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.241][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.242][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.246][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.248][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.249][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.250][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.261][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.DEBUG[2025-08-15 00:02:06.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.267][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.269][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.284][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.292][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.293][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.300][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:06.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.308][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:06.311][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-15 00:02:06.320][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-15 00:02:06.322][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:06.324][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-15 00:02:06.325][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:06.326][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:06.327][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:06.329][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:06.330][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:06.331][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-15 00:02:06.332][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-15 00:02:06.334][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:06.335][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:06.336][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-15 00:02:06.337][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-15 00:02:06.339][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-15 00:02:06.340][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:06.341][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:02:06.341][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:02:06.341][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:02:06.343][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-15 00:02:06.344][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:06.345][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:06.346][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:06.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:06.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:06.350][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:06.351][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:02:06.351][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-15 00:02:06.352][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:06.353][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:06.354][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:06.356][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-15 00:02:06.356][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-15 00:02:06.363][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:02:06.365][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:02:06.367][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-15 00:02:06.369][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:02:06.371][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:02:06.373][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:02:06.427][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-15 00:02:06.429][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-15 00:02:06.433][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-15 00:02:06.437][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-15 00:02:06.442][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:02:06.443][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:02:06.445][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-15 00:02:06.446][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-15 00:02:06.457][biodb::testThat]
biodb.INFO [2025-08-15 00:02:06.458][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2025-08-15 00:02:06.459][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:06.460][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:06.517][loadFileContents] Loaded 1 files from cache: [1]: "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/testref/entry-chebi-15440-content.xml".
biodb.DEBUG[2025-08-15 00:02:06.519][biodb$getFactory()$createEntryFromCo ...] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-15 00:02:06.522][biodb$getFactory()$createEntryFromCo ...] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-15 00:02:06.530][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:06.531][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:06.533][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:06.557][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:06.558][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:06.559][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:06.560][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:06.569][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.571][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.572][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.573][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.591][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:06.592][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:06.593][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.594][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.620][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:06.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:06.623][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.624][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.625][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:06.626][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:06.628][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.629][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.630][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:06.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:06.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.636][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:06.637][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:06.638][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.639][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:06.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:06.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.646][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.647][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.648][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.649][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.651][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.656][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:06.658][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:06.659][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.660][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.662][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:06.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:06.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.678][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:06.680][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:06.681][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.682][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.684][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:06.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:06.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.689][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:06.690][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:06.691][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.693][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:06.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:06.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.699][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:06.701][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:06.702][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.703][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.705][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:06.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:06.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.710][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:06.711][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:06.713][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.714][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.715][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:06.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:06.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.720][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:06.722][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:06.723][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.724][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.726][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:06.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:06.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.731][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.736][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.741][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.742][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.746][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.756][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.794][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.804][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:06.809][biodb$getFactory()$createEntryFromCo ...] Accession numbers: 15440.
biodb.TRACE[2025-08-15 00:02:06.816][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:06.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:06.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.822][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:06.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:06.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.852][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.854][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.855][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.858][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:06.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.863][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:06.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:06.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.868][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:06.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:06.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.873][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-15 00:02:06.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-15 00:02:06.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.879][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-15 00:02:06.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-15 00:02:06.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.884][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-15 00:02:06.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-15 00:02:06.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.889][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-15 00:02:06.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-15 00:02:06.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.947][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.976][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.977][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.978][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.979][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.981][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.986][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:06.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:06.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.991][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:06.996][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:06.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:06.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.001][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.031][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.036][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.038][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.039][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.040][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.041][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.061][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.066][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.067][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.068][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.076][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.077][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.080][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.081][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:07.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:07.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:07.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.108][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:07.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:07.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.113][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:07.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:07.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.118][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:07.119][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:07.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.121][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.123][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:07.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:07.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.151][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.156][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.161][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.167][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.168][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.169][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.170][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.172][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.203][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.208][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.210][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.211][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.217][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.219][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.234][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.240][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.242][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.243][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.250][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.251][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.252][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.253][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.270][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.275][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.280][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.285][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.286][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.287][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.288][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.290][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.311][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.316][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.321][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.326][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.327][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.329][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.330][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.331][self$getBiodb()$getEntryFields()$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.352][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.357][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.359][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.360][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.361][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.362][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.365][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.367][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.368][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.370][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.371][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.372][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.387][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:07.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:07.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.392][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:07.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:07.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.397][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:07.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:07.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.406][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.407][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:07.409][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:07.410][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.411][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.412][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:07.414][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:07.415][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.416][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.433][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.439][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.444][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.449][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.450][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.452][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.453][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.454][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.476][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:07.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.482][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:07.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.486][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:07.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.492][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.493][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:07.494][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.495][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.497][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:07.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.668][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.672][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.692][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.694][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.696][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.697][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.705][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.707][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.708][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.710][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.721][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.723][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:07.724][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.725][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.734][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.736][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:07.737][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.738][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.747][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.748][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:07.750][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.751][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.762][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.764][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:07.765][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.766][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.779][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.781][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:07.782][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.783][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.791][ef$get] Asked field names are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.792][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:07.794][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.800][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.808][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:07.809][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:07.810][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.812][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.824][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:07.826][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:07.827][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.828][ef$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:07.853][biodb::testThat]
biodb.INFO [2025-08-15 00:02:07.854][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2025-08-15 00:02:07.856][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:07.857][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:07.872][private$loadEntries] Creating entries from ids [1]: "15440".
biodb.DEBUG[2025-08-15 00:02:07.879][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-15 00:02:07.886][cch$loadFileContent] Trying to load 1 files from cache: [1]: "15440".
biodb.TRACE[2025-08-15 00:02:07.888][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:07.891][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/15440.xml".
biodb.DEBUG[2025-08-15 00:02:07.894][conn$getEntryContent] 1 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-15 00:02:07.923][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-15 00:02:07.925][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-15 00:02:07.927][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:07.928][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:07.929][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:07.937][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:07.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:07.939][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:07.941][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:07.944][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.945][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.946][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.947][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.949][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:07.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:07.952][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.953][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.969][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.971][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.972][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.973][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.975][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:07.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:07.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.987][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.988][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.989][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.990][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.992][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:07.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:07.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:07.996][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:07.997][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:07.999][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:08.000][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.001][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.003][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:08.004][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:08.005][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.008][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:08.009][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:08.011][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.012][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.013][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:08.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:08.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.019][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:08.020][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:08.021][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.022][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.024][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:08.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:08.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.029][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:08.031][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:08.032][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.033][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.035][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:08.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:08.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.040][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:08.041][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:08.042][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.044][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.045][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:08.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:08.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.051][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:08.052][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:08.053][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.054][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:08.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:08.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:08.063][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:08.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.065][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.067][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:08.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:08.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.072][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.074][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:08.076][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:08.078][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.080][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.082][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:08.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:08.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.087][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:08.089][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:08.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.092][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:08.094][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:08.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.097][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:08.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:08.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.117][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.123][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.132][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:08.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:08.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:08.137][self$createEntryFromContent] Accession numbers: 15440.
biodb.TRACE[2025-08-15 00:02:08.139][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2025-08-15 00:02:08.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2025-08-15 00:02:08.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.144][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2025-08-15 00:02:08.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2025-08-15 00:02:08.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.148][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2025-08-15 00:02:08.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2025-08-15 00:02:08.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:08.585][biodb::testThat]
biodb.INFO [2025-08-15 00:02:08.587][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2025-08-15 00:02:08.589][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:08.591][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:08.597][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:08.601][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:08.603][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.605][ef$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:08.608][function(conn, opt)] Testing searchForEntries() with entry "15440" and field "name".
biodb.TRACE[2025-08-15 00:02:08.655][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:08.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:08.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.660][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:08.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:08.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:08.665][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:08.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:08.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:08.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:08.673][function(conn, opt)] With value "squalene".
biodb.DEBUG[2025-08-15 00:02:08.680][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-15 00:02:08.704][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:08.718][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-15 00:02:08.720][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:08.724][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-15 00:02:08.752][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[2025-08-15 00:02:08.757][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:08.758][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:08.761][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:09.201][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL%20NAMES&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:02:09.497][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:09.500][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content"
biodb.TRACE[2025-08-15 00:02:09.523][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.request"
biodb.DEBUG[2025-08-15 00:02:09.528][function(conn, opt)] With found IDs none.
biodb.TRACE[2025-08-15 00:02:09.911][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:09.913][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:09.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:09.915][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:09.917][ef$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:09.918][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:09.919][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:09.920][ef$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:09.952][biodb::testThat]
biodb.INFO [2025-08-15 00:02:09.954][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2025-08-15 00:02:09.955][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:09.956][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:10.003][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:10.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:10.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.011][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:10.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:10.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.018][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:10.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:10.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:10.375][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:10.379][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:10.381][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:10.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:10.388][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.INFO [2025-08-15 00:02:10.491][biodb::testThat]
biodb.INFO [2025-08-15 00:02:10.494][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2025-08-15 00:02:10.496][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:10.498][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:10.540][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:10.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:10.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.549][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:10.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:10.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.558][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.567][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.575][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.584][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.592][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.599][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.601][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.608][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.610][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-15 00:02:10.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-15 00:02:10.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.617][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-15 00:02:10.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-15 00:02:10.620][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.621][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.641][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:10.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:10.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.646][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.647][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:10.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:10.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.653][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.658][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:10.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.670][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:10.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.675][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.681][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.682][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2025-08-15 00:02:10.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.686][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2025-08-15 00:02:10.688][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2025-08-15 00:02:10.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:10.692][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2025-08-15 00:02:10.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2025-08-15 00:02:10.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:10.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:10.713][biodb::testThat]
biodb.INFO [2025-08-15 00:02:10.714][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2025-08-15 00:02:10.716][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:10.717][biodb::testThat]
biodb.INFO [2025-08-15 00:02:10.737][biodb::testThat]
biodb.INFO [2025-08-15 00:02:10.739][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2025-08-15 00:02:10.740][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:10.742][biodb::testThat]
biodb.INFO [2025-08-15 00:02:10.765][biodb::testThat]
biodb.INFO [2025-08-15 00:02:10.768][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2025-08-15 00:02:10.770][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:10.772][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:10.780][function(conn, opt)] Trying to download "https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440".
biodb.DEBUG[2025-08-15 00:02:11.743][getUrlContent] Use RCurl for downloading content of URL https://www.ebi.ac.uk/chebi/searchId.do?chebiId=15440.
biodb.INFO [2025-08-15 00:02:13.113][biodb::testThat]
biodb.INFO [2025-08-15 00:02:13.115][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2025-08-15 00:02:13.117][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:13.118][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:13.424][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[2025-08-15 00:02:13.766][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:13.768][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:13.769][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:13.770][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:13.772][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:13.773][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:13.775][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:13.776][ef$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:13.779][biodb::testThat]
biodb.INFO [2025-08-15 00:02:13.780][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2025-08-15 00:02:13.782][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:13.783][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:13.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:13.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:13.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:13.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:13.807][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:13.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:13.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:13.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:13.812][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:13.981][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:13.985][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:13.987][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:13.989][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:13.992][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-15 00:02:14.067][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:14.071][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:14.073][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:14.075][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:14.078][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-15 00:02:14.151][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-15 00:02:14.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-15 00:02:14.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:14.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:14.174][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:14.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:14.183][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:14.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:14.188][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:14.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:14.193][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:14.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:14.198][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.200][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:14.201][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:14.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:14.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:14.225][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:14.226][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:14.240][private$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[2025-08-15 00:02:14.530][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[2025-08-15 00:02:14.822][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:14.826][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content"
biodb.TRACE[2025-08-15 00:02:14.834][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.request"
biodb.DEBUG[2025-08-15 00:02:14.841][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[2025-08-15 00:02:14.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:14.849][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:14.851][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:15.139][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:02:15.440][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:15.443][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content"
biodb.TRACE[2025-08-15 00:02:15.448][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.request"
biodb.DEBUG[2025-08-15 00:02:15.465][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:15.469][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:15.470][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:15.472][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:15.774][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74%2A&searchCategory=MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:02:16.067][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:16.070][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content"
biodb.TRACE[2025-08-15 00:02:16.076][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.request"
biodb.DEBUG[2025-08-15 00:02:16.129][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[2025-08-15 00:02:16.133][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:16.135][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-15 00:02:16.137][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:16.141][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-15 00:02:16.145][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[2025-08-15 00:02:16.149][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:16.150][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-15 00:02:16.152][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:16.155][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-15 00:02:16.158][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:16.162][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:16.163][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2025-08-15 00:02:16.165][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:16.168][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.DEBUG[2025-08-15 00:02:16.217][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[2025-08-15 00:02:16.232][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:16.234][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:16.236][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:16.239][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-15 00:02:16.302][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[2025-08-15 00:02:16.306][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:16.308][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:16.309][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:16.312][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-15 00:02:16.370][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:16.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:16.375][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.378][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:16.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:16.380][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:16.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:16.385][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:16.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:16.390][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:16.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:16.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:16.399][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[2025-08-15 00:02:16.403][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:16.404][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:16.406][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:16.694][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:02:16.990][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:16.993][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content"
biodb.TRACE[2025-08-15 00:02:16.998][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.request"
biodb.DEBUG[2025-08-15 00:02:17.003][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:17.007][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:17.009][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:17.011][private$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[2025-08-15 00:02:17.301][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[2025-08-15 00:02:17.604][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:17.609][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content"
biodb.TRACE[2025-08-15 00:02:17.617][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.request"
biodb.DEBUG[2025-08-15 00:02:17.622][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:17.627][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:17.628][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:17.630][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:17.927][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:02:18.221][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:18.226][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e98fcf727dab60128a5496d811825b6a.content"
biodb.TRACE[2025-08-15 00:02:18.232][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e98fcf727dab60128a5496d811825b6a.request"
biodb.DEBUG[2025-08-15 00:02:18.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39124*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.284][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.286][cch$loadFileContent] Trying to load 1 files from cache: [1]: "c5171beada848a87ef2ffa10427d9be3".
biodb.TRACE[2025-08-15 00:02:18.288][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.291][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/c5171beada848a87ef2ffa10427d9be3.content".
biodb.DEBUG[2025-08-15 00:02:18.295][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39125*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.298][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.300][cch$loadFileContent] Trying to load 1 files from cache: [1]: "750e63ff76a843f016511fa71c89113e".
biodb.TRACE[2025-08-15 00:02:18.302][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.307][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/750e63ff76a843f016511fa71c89113e.content".
biodb.DEBUG[2025-08-15 00:02:18.310][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39126*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.314][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.316][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e98fcf727dab60128a5496d811825b6a".
biodb.TRACE[2025-08-15 00:02:18.318][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.322][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/e98fcf727dab60128a5496d811825b6a.content".
biodb.DEBUG[2025-08-15 00:02:18.383][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.389][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.391][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:18.393][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.396][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.DEBUG[2025-08-15 00:02:18.477][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=squalene&searchCategory=ALL NAMES&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.481][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.483][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b9623d99e42a57d0f12e83910c2ffbf2".
biodb.TRACE[2025-08-15 00:02:18.485][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.487][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b9623d99e42a57d0f12e83910c2ffbf2.content".
biodb.TRACE[2025-08-15 00:02:18.564][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-15 00:02:18.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-15 00:02:18.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:18.585][biodb::testThat]
biodb.INFO [2025-08-15 00:02:18.586][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2025-08-15 00:02:18.587][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:18.589][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:18.592][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-15 00:02:18.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-15 00:02:18.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.598][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.605][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.611][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.613][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:18.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:18.624][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:18.625][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:18.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:18.634][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:18.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:18.636][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:18.638][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:18.641][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.645][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.648][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-15 00:02:18.650][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.653][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-15 00:02:18.657][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.660][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.662][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-15 00:02:18.664][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.667][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-15 00:02:18.672][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.677][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:18.678][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2025-08-15 00:02:18.681][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:18.684][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.TRACE[2025-08-15 00:02:18.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.708][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.717][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:18.722][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:18.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:18.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:18.776][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:18.777][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:18.779][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:18.786][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:18.788][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:18.789][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:18.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:18.793][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:18.797][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:18.799][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:18.801][private$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[2025-08-15 00:02:21.803][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:21.806][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:21.809][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:21.812][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:22.095][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:22.097][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:22.099][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:22.103][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:22.399][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:22.400][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:22.402][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:22.404][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:22.792][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:22.794][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:22.795][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:22.797][private$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[2025-08-15 00:02:23.080][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:23.082][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:23.085][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:23.088][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:23.367][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:23.369][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:23.371][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:23.374][private$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[2025-08-15 00:02:23.662][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:23.664][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:23.667][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:23.669][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:23.946][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:23.947][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:23.948][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:23.951][private$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[2025-08-15 00:02:24.235][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:24.236][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:24.238][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:24.240][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:24.517][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:24.519][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:24.521][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:24.525][private$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[2025-08-15 00:02:24.817][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:24.818][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:24.820][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:24.822][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:25.097][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:25.099][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:25.101][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:25.104][private$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[2025-08-15 00:02:25.387][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:25.388][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:25.390][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:25.392][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:25.668][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:25.669][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:25.671][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:25.673][private$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[2025-08-15 00:02:25.953][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:25.955][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:25.957][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:25.959][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:26.239][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:26.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:26.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:26.244][private$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[2025-08-15 00:02:26.527][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:26.529][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:26.531][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:26.532][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:26.824][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.DEBUG[2025-08-15 00:02:26.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:26.827][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:26.829][private$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[2025-08-15 00:02:27.116][doesRCurlRequestUrlExist] According to RCurl, URL https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL does not exist.
biodb.TRACE[2025-08-15 00:02:27.117][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2025-08-15 00:02:27.119][getUrlRequestResult] URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2025-08-15 00:02:27.121][getBaseUrlRequestResult] Using base::url() 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.INFO [2025-08-15 00:02:27.401][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL". Retrying connection to server...
biodb.INFO [2025-08-15 00:02:27.431][biodb::testThat]
biodb.INFO [2025-08-15 00:02:27.433][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2025-08-15 00:02:27.435][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:27.438][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:27.444][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-15 00:02:27.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-15 00:02:27.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.453][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.461][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.470][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.478][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:27.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:27.491][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:27.493][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:27.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:27.503][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:27.505][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:27.506][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:27.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:27.511][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:27.515][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:27.517][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-15 00:02:27.519][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:27.522][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-15 00:02:27.525][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:27.529][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:27.531][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-15 00:02:27.533][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:27.535][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-15 00:02:27.539][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:27.543][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:27.544][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2025-08-15 00:02:27.546][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:27.549][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.TRACE[2025-08-15 00:02:27.598][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.606][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.614][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.616][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:27.621][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:27.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:27.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:27.633][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:27.634][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:27.636][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:27.650][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:27.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:27.653][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:27.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:27.658][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:27.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:27.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:27.666][private$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[2025-08-15 00:02:28.123][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[2025-08-15 00:02:28.424][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:28.427][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content"
biodb.TRACE[2025-08-15 00:02:28.432][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.request"
biodb.DEBUG[2025-08-15 00:02:28.437][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[2025-08-15 00:02:28.441][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:28.442][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:28.444][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:28.772][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39%2A&searchCategory=MONOISOTOPIC%20MASS&maximumResults=0&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:02:29.066][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:29.069][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content"
biodb.TRACE[2025-08-15 00:02:29.075][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.request"
biodb.DEBUG[2025-08-15 00:02:29.079][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:29.080][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:29.081][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:29.088][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:29.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:29.091][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:29.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:29.094][private$loadEntries] Creating entries from ids [1]: "4648".
biodb.DEBUG[2025-08-15 00:02:29.134][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-15 00:02:29.137][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4648".
biodb.TRACE[2025-08-15 00:02:29.138][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-15 00:02:29.140][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-15 00:02:29.141][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-15 00:02:29.142][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:02:29.144][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-15 00:02:29.145][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-15 00:02:29.148][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:29.150][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:29.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:29.159][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:29.160][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:29.161][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:29.162][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:29.164][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.DEBUG[2025-08-15 00:02:29.167][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:29.169][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:29.170][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648".
biodb.TRACE[2025-08-15 00:02:29.735][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=4648).
biodb.DEBUG[2025-08-15 00:02:30.048][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:30.051][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.content"
biodb.TRACE[2025-08-15 00:02:30.056][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/844829d8afb6d338ebac906e62f6cb8e.request"
biodb.TRACE[2025-08-15 00:02:30.060][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/4648.xml"
biodb.DEBUG[2025-08-15 00:02:30.063][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-15 00:02:30.064][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-15 00:02:30.066][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-15 00:02:30.068][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:30.069][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:30.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:30.095][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:30.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:30.098][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:30.099][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:30.102][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.103][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.105][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.106][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.112][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:30.114][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:30.115][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.116][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.118][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:30.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:30.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.123][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:30.124][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:30.125][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.126][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.128][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:30.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:30.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.133][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:30.134][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:30.135][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.137][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.138][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:30.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:30.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.143][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:30.144][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:30.146][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.147][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.148][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:30.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:30.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.153][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:30.155][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:30.156][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.157][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.159][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:30.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:30.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.164][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:30.165][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:30.166][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.167][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.169][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:30.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:30.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.174][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.175][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.176][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.177][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.179][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.184][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:30.186][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:30.187][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.188][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:30.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:30.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.195][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:30.196][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:30.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.198][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.200][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:30.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:30.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.205][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:30.206][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:30.207][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.209][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.210][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:30.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:30.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.215][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:30.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:30.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.220][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:30.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:30.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.230][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:30.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:30.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.235][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.240][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.245][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.260][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:30.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:30.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:30.266][self$createEntryFromContent] Accession numbers: 4648.
biodb.TRACE[2025-08-15 00:02:30.274][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.280][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.285][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.288][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:30.291][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:30.292][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:30.293][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:30.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:30.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:30.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:30.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:30.318][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.323][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:30.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:30.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:30.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:30.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:30.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:30.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:30.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:30.347][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:30.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:30.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:30.351][private$loadEntries] Creating entries from ids [1]: "62447".
biodb.DEBUG[2025-08-15 00:02:30.352][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-15 00:02:30.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "62447".
biodb.TRACE[2025-08-15 00:02:30.356][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-15 00:02:30.357][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-15 00:02:30.359][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-15 00:02:30.360][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:02:30.361][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-15 00:02:30.362][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-15 00:02:30.375][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:30.377][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:30.378][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:30.387][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:30.389][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:30.390][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:30.391][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:30.393][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.DEBUG[2025-08-15 00:02:30.396][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:30.397][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:30.399][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447".
biodb.TRACE[2025-08-15 00:02:30.909][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=62447).
biodb.DEBUG[2025-08-15 00:02:31.220][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:31.222][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.content"
biodb.TRACE[2025-08-15 00:02:31.228][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/ceadc6ac0ce91f601616e22be7c76851.request"
biodb.TRACE[2025-08-15 00:02:31.232][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/62447.xml"
biodb.DEBUG[2025-08-15 00:02:31.234][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-15 00:02:31.236][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-15 00:02:31.237][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-15 00:02:31.239][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.240][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.242][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.251][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:31.257][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.259][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.260][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.261][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.268][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:31.269][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:31.270][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.272][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.273][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:31.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:31.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.278][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:31.280][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:31.281][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.282][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.284][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:31.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:31.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.289][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:31.290][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:31.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.293][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.294][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:31.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:31.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.300][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:31.301][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:31.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.303][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.305][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:31.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:31.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.310][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:31.311][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:31.312][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.314][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.315][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:31.316][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.318][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.319][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.320][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:31.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.325][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.327][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.328][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.330][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.331][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.336][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:31.337][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:31.339][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.340][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.342][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:31.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:31.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.347][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:31.349][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:31.350][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.351][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.353][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:31.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:31.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.358][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:31.359][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:31.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.361][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.363][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:31.364][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:31.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.368][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.372][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.373][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.378][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.383][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.393][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.398][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.401][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.402][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.403][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.408][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.410][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.411][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.412][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.413][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:31.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:31.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:31.418][self$createEntryFromContent] Accession numbers: 62447.
biodb.TRACE[2025-08-15 00:02:31.420][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.430][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:31.435][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-15 00:02:31.437][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.438][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.440][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.447][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.449][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.450][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:31.453][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.458][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.463][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.464][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-15 00:02:31.466][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-15 00:02:31.467][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-15 00:02:31.468][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.469][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.473][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.474][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.476][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.477][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.478][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.479][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.481][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.482][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.483][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.484][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.486][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.487][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-15 00:02:31.488][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.490][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.492][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.493][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.498][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.512][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-15 00:02:31.514][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.515][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.516][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.527][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.531][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.533][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:31.535][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.543][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.545][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.552][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.554][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-15 00:02:31.555][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-15 00:02:31.557][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-15 00:02:31.559][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.561][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.563][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.565][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.567][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.569][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.571][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.573][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.575][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.577][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.579][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.581][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.583][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.585][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.587][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.589][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-15 00:02:31.591][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.599][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.601][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.607][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.616][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-15 00:02:31.618][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.620][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.632][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.634][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.635][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:31.638][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.643][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.651][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.653][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-15 00:02:31.655][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-15 00:02:31.656][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-15 00:02:31.658][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.660][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.662][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.664][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.666][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.668][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.670][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.671][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.672][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.673][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.674][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:31.676][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.677][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.686][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.688][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.689][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-15 00:02:31.691][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.696][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:31.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.706][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-15 00:02:31.707][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-15 00:02:31.708][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-15 00:02:31.724][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-15 00:02:31.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-15 00:02:31.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:31.737][biodb::testThat]
biodb.INFO [2025-08-15 00:02:31.739][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2025-08-15 00:02:31.741][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:31.743][biodb::testThat]
biodb.TRACE[2025-08-15 00:02:31.749][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2025-08-15 00:02:31.751][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2025-08-15 00:02:31.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.756][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.762][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.767][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.772][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:31.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:31.782][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.802][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:31.809][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.72*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:31.813][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:31.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "dabc9e8530050c4ceebbaec76743bcf1".
biodb.TRACE[2025-08-15 00:02:31.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:31.820][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/dabc9e8530050c4ceebbaec76743bcf1.content".
biodb.DEBUG[2025-08-15 00:02:31.824][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.73*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:31.828][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:31.830][cch$loadFileContent] Trying to load 1 files from cache: [1]: "41b7f9723242a79cfe14bebd91dbb5b6".
biodb.TRACE[2025-08-15 00:02:31.832][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:31.834][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/41b7f9723242a79cfe14bebd91dbb5b6.content".
biodb.DEBUG[2025-08-15 00:02:31.838][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.74*&searchCategory=MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:31.842][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:31.843][cch$loadFileContent] Trying to load 1 files from cache: [1]: "94c7655c8f372fb2982c15119402bcba".
biodb.TRACE[2025-08-15 00:02:31.845][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:31.848][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/94c7655c8f372fb2982c15119402bcba.content".
biodb.TRACE[2025-08-15 00:02:31.893][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.898][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.904][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.905][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.908][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:31.917][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.918][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.927][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.930][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.931][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:31.934][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.38*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:31.938][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:31.940][cch$loadFileContent] Trying to load 1 files from cache: [1]: "49f51d93ac229648aa454636918ce386".
biodb.TRACE[2025-08-15 00:02:31.942][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:31.944][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/49f51d93ac229648aa454636918ce386.content".
biodb.DEBUG[2025-08-15 00:02:31.948][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=410.39*&searchCategory=MONOISOTOPIC MASS&maximumResults=0&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:31.953][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:02:31.954][cch$loadFileContent] Trying to load 1 files from cache: [1]: "121ea95906eb67bed88948c362686e4f".
biodb.TRACE[2025-08-15 00:02:31.956][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:02:31.959][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/121ea95906eb67bed88948c362686e4f.content".
biodb.DEBUG[2025-08-15 00:02:31.962][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:31.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:31.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:31.979][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:31.981][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:31.982][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:31.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:31.987][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:31.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:31.995][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:31.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.004][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:32.012][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:32.014][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:32.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:32.036][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:32.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:32.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:32.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:32.041][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.042][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.043][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.046][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.051][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:32.056][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:32.057][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:32.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:32.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:32.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:32.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:32.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:32.134][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.139][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.141][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.142][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.144][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.146][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:32.147][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.148][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:32.150][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2025-08-15 00:02:32.171][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:32.172][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:32.173][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:32.248][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:32.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:32.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:32.252][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:32.264][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.293][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.294][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-15 00:02:32.296][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-15 00:02:32.297][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-15 00:02:32.298][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.300][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.301][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.302][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.303][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.305][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.306][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.307][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.308][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.310][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.319][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.320][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.322][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.323][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.324][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.326][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-15 00:02:32.327][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.333][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.338][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.344][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [4648].
biodb.DEBUG[2025-08-15 00:02:32.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:32.346][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:32.354][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:32.362][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:32.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:32.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:32.366][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.TRACE[2025-08-15 00:02:32.367][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.372][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.380][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.382][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-15 00:02:32.383][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-15 00:02:32.385][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-15 00:02:32.386][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.387][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.388][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.390][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.391][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.392][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.394][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.395][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.396][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.397][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.398][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.400][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.401][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.402][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.403][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.404][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-15 00:02:32.406][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.411][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.416][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.421][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [15440].
biodb.DEBUG[2025-08-15 00:02:32.422][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:32.423][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:32.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:32.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:32.435][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:32.436][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:32.437][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:32.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.444][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.450][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.451][private$selectFields] Fields type: <NULL>
biodb.TRACE[2025-08-15 00:02:32.452][private$selectFields] Fields is null: FALSE
biodb.TRACE[2025-08-15 00:02:32.454][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2025-08-15 00:02:32.455][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.456][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.458][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.459][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.461][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.462][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.463][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.464][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.466][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.467][private$selectFields] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.468][private$organizeFieldsByGroups] Fields [1]: "chebi.id"
biodb.TRACE[2025-08-15 00:02:32.470][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.471][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.472][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.473][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.475][private$organizeFieldsByGroups] Groups [2]: "chebi.id, list()"
biodb.TRACE[2025-08-15 00:02:32.476][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.481][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.486][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:32.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:32.492][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [chebi.id] [62447].
biodb.DEBUG[2025-08-15 00:02:32.493][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2025-08-15 00:02:32.494][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2025-08-15 00:02:32.536][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2025-08-15 00:02:32.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2025-08-15 00:02:32.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:32.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:32.549][biodb::testThat]
biodb.INFO [2025-08-15 00:02:32.551][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2025-08-15 00:02:32.553][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:32.555][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:32.558][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2025-08-15 00:02:32.561][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-15 00:02:32.564][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.INFO [2025-08-15 00:02:32.566][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-08-15 00:02:32.570][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-15 00:02:32.572][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-15 00:02:32.574][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-15 00:02:32.576][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:02:32.578][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-15 00:02:32.580][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-15 00:02:32.585][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:32.587][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:32.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:32.616][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:32.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:32.619][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:32.620][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:32.621][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.DEBUG[2025-08-15 00:02:32.625][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:32.626][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:32.628][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA".
biodb.TRACE[2025-08-15 00:02:32.944][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGA).
biodb.DEBUG[2025-08-15 00:02:33.253][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:33.258][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.content"
biodb.TRACE[2025-08-15 00:02:33.265][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b5b4e4941cdc7bc8ff5e29f921c1e9db.request"
biodb.TRACE[2025-08-15 00:02:33.272][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGA.xml"
biodb.DEBUG[2025-08-15 00:02:33.275][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-15 00:02:33.278][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-15 00:02:33.281][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-15 00:02:33.284][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:33.286][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:33.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:33.300][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:33.302][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:33.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:33.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:33.311][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.313][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.315][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.317][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.328][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:33.330][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:33.332][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.334][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.336][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:33.338][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:33.340][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.342][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.345][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:33.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:33.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.351][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.353][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:33.355][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:33.357][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.359][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.361][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:33.363][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:33.366][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.367][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.370][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:33.372][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:33.374][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.376][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.378][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:33.381][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:33.383][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.384][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.387][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:33.389][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:33.391][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.393][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.396][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:33.398][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:33.400][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.402][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.404][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:33.406][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:33.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.410][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.413][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:33.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:33.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.421][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:33.423][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:33.425][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.429][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.437][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:33.439][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:33.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.453][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.459][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.467][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.470][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.477][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:33.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:33.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:33.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:33.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:33.493][self$createEntryFromContent] Accession numbers: .
biodb.DEBUG[2025-08-15 00:02:33.495][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2025-08-15 00:02:33.514][biodb::testThat]
biodb.INFO [2025-08-15 00:02:33.516][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2025-08-15 00:02:33.517][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:33.518][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:33.531][function(conn, opt)] IDS: [4]: "WRONGB, 15440, 2528, 7799"
biodb.DEBUG[2025-08-15 00:02:33.533][private$loadEntries] Creating entries from ids [3]: "WRONGB, 2528, 7799".
biodb.DEBUG[2025-08-15 00:02:33.536][conn$getEntryContent] Get ChEBI entry content(s) for 3 id(s)...
biodb.TRACE[2025-08-15 00:02:33.539][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, 2528, 7799".
biodb.TRACE[2025-08-15 00:02:33.542][cch$loadFileContent] file.exist = [3]: "FALSE, FALSE, FALSE".
biodb.TRACE[2025-08-15 00:02:33.544][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-15 00:02:33.547][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-15 00:02:33.549][conn$getEntryContent] 3 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:02:33.551][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-15 00:02:33.553][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-15 00:02:33.560][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:33.562][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:33.564][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:33.592][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:33.594][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:33.596][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:33.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:33.601][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.DEBUG[2025-08-15 00:02:33.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:33.608][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:33.611][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB".
biodb.TRACE[2025-08-15 00:02:48.615][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=WRONGB).
biodb.DEBUG[2025-08-15 00:02:50.645][scheduler$sendRequest] Saving content of request to cache.
biodb.INFO [2025-08-15 00:02:50.648][self$getFolderPath] Create cache folder "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649" for "chebi-0c5076ac2a43d16dbce503a44b09f649".
biodb.TRACE[2025-08-15 00:02:50.651][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.content"
biodb.TRACE[2025-08-15 00:02:50.657][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/32348f2b7cfb460a97c8a8aa145f239f.request"
biodb.DEBUG[2025-08-15 00:02:50.660][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:50.662][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:50.664][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:50.674][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:50.677][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:50.678][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:50.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:50.683][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.DEBUG[2025-08-15 00:02:50.689][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:50.690][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:50.692][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528".
biodb.TRACE[2025-08-15 00:02:51.563][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2528).
biodb.DEBUG[2025-08-15 00:02:51.909][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:51.913][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.content"
biodb.TRACE[2025-08-15 00:02:51.918][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/65267cab26ad2d71ed08b12751f9bef2.request"
biodb.DEBUG[2025-08-15 00:02:51.921][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:51.922][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:51.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:51.934][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:51.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:51.938][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:51.940][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[2025-08-15 00:02:51.942][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.DEBUG[2025-08-15 00:02:51.945][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:51.947][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:51.950][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799".
biodb.TRACE[2025-08-15 00:02:52.420][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=7799).
biodb.DEBUG[2025-08-15 00:02:52.832][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:52.837][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.content"
biodb.TRACE[2025-08-15 00:02:52.844][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/07eb1d5438367a7b1616709944d88b07.request"
biodb.TRACE[2025-08-15 00:02:52.851][private$doSaveContentToFile] Saving to cache [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/WRONGB.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2528.xml, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7799.xml"
biodb.DEBUG[2025-08-15 00:02:52.875][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-15 00:02:52.878][self$createEntryFromContent] Creating ChEBI entries from 3 content(s).
biodb.DEBUG[2025-08-15 00:02:52.880][self$createEntryFromContent] Parsing 3 ChEBI entries.
biodb.DEBUG[2025-08-15 00:02:52.883][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:52.885][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:52.887][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:52.900][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:52.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:52.904][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:52.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:52.910][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:52.913][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:52.914][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.916][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.918][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:52.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:52.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.925][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:52.926][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:52.927][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.928][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.930][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:52.932][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:52.933][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.935][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.936][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:52.938][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:52.939][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.941][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.942][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:52.944][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:52.945][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.946][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.948][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:52.950][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:52.952][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.954][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.957][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:52.959][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:52.961][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.963][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.966][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:52.968][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:52.970][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.972][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.974][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:52.976][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:52.978][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.980][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.983][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:52.986][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:52.988][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:52.990][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:52.993][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:52.996][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:52.998][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.000][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.003][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.012][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.029][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.038][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.040][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.046][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.053][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:53.062][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:53.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:53.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:53.076][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:53.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:53.079][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:53.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:53.083][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.084][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.086][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.087][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.088][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.090][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.091][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.094][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:53.095][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:53.097][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.098][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.100][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:53.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:53.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.104][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.105][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:53.107][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:53.108][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.109][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.111][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:53.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:53.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.117][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:53.118][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:53.120][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.121][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.122][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:53.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:53.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.128][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.130][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.131][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.132][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.134][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.140][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.141][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.143][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.145][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.147][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.148][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.149][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.151][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.152][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:53.154][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:53.155][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.156][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.158][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:53.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:53.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.164][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.166][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.168][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.170][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.173][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.181][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:53.184][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:53.186][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.187][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.189][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:53.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:53.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.195][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:53.196][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:53.197][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.198][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.200][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:53.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:53.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.204][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.205][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:53.207][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:53.208][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.209][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.211][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:53.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:53.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.217][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.219][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.223][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.226][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.235][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.243][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.250][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.253][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.254][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.257][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:53.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:53.264][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:53.265][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:53.276][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:53.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:53.281][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:53.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:02:53.287][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.290][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.292][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.294][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.307][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:53.309][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:53.311][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.314][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.316][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:02:53.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:02:53.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.326][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:53.328][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:53.330][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.332][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:02:53.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:02:53.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.344][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:53.347][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:53.349][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.351][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.353][self$getBiodb()$getEntryFields()$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:02:53.354][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:02:53.355][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.356][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.358][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.359][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.360][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.362][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.363][self$getBiodb()$getEntryFields()$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:02:53.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.369][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.371][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.373][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.375][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.377][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:02:53.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.381][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.383][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:53.384][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:53.386][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.387][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.388][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:02:53.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:02:53.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.394][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.395][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.396][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.398][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.399][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:53.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.405][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:53.406][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:53.408][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.410][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:53.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:53.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.423][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:53.426][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:53.427][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.429][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.431][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:02:53.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:02:53.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.441][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:53.443][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:53.446][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.448][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.451][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:02:53.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:02:53.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.461][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.466][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.468][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.470][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.478][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.487][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:02:53.491][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.504][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.506][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.512][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.521][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.530][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.539][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.544][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.548][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.566][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.580][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.585][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:53.604][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:02:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:02:53.609][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:53.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:02:53.613][self$createEntryFromContent] Accession numbers: , 2528, 7799.
biodb.DEBUG[2025-08-15 00:02:53.615][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2025-08-15 00:02:53.617][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2025-08-15 00:02:53.652][biodb::testThat]
biodb.INFO [2025-08-15 00:02:53.654][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2025-08-15 00:02:53.657][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:53.659][biodb::testThat]
biodb.INFO [2025-08-15 00:02:53.861][biodb::testThat]
biodb.INFO [2025-08-15 00:02:53.862][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2025-08-15 00:02:53.864][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:53.865][biodb::testThat]
biodb.INFO [2025-08-15 00:02:53.891][biodb::testThat]
biodb.INFO [2025-08-15 00:02:53.894][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2025-08-15 00:02:53.896][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:53.898][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:53.903][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=1*&searchCategory=CHEBI ID&maximumResults=100&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:53.908][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:53.910][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:53.914][private$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[2025-08-15 00:02:54.720][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[2025-08-15 00:02:55.114][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:55.117][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.content"
biodb.TRACE[2025-08-15 00:02:55.123][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/aed2cd6d5d221333c0a30a9f8dbc41b4.request"
biodb.TRACE[2025-08-15 00:02:55.233][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:02:55.236][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:02:55.238][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:55.240][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:02:55.242][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:55.244][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:02:55.246][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:02:55.248][ef$get] fields variable is a list.
biodb.INFO [2025-08-15 00:02:55.252][biodb::testThat]
biodb.INFO [2025-08-15 00:02:55.254][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2025-08-15 00:02:55.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:55.257][biodb::testThat]
biodb.ERROR[2025-08-15 00:02:55.284][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2025-08-15 00:02:55.305][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2025-08-15 00:02:55.329][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-15 00:02:55.332][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-15 00:02:55.335][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-15 00:02:55.337][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-15 00:02:55.339][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:55.341][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:55.343][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.346][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-15 00:02:55.367][biodb::testContext]
biodb.INFO [2025-08-15 00:02:55.369][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:02:55.371][biodb::testContext] Test context - Test conversions
biodb.INFO [2025-08-15 00:02:55.373][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:02:55.375][biodb::testContext]
biodb.INFO [2025-08-15 00:02:55.380][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:02:55.384][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-15 00:02:55.392][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:02:55.395][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-15 00:02:55.397][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-15 00:02:55.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.403][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.405][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-15 00:02:55.407][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-15 00:02:55.409][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.412][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[2025-08-15 00:02:55.415][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-15 00:02:55.417][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-15 00:02:55.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.424][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-15 00:02:55.426][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-15 00:02:55.428][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-15 00:02:55.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.435][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-15 00:02:55.437][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-15 00:02:55.440][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-15 00:02:55.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.448][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-15 00:02:55.450][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-15 00:02:55.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.459][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-15 00:02:55.462][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-15 00:02:55.464][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-15 00:02:55.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.472][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-15 00:02:55.475][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-15 00:02:55.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.480][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.483][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-15 00:02:55.485][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-15 00:02:55.487][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-15 00:02:55.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.491][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.493][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.495][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:02:55.497][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-15 00:02:55.499][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-15 00:02:55.501][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-15 00:02:55.503][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-15 00:02:55.505][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-15 00:02:55.507][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.511][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.513][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-15 00:02:55.515][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-15 00:02:55.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.520][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-15 00:02:55.521][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-15 00:02:55.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.524][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[2025-08-15 00:02:55.526][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-15 00:02:55.527][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-15 00:02:55.528][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.529][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.532][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-15 00:02:55.533][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-15 00:02:55.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.538][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-15 00:02:55.540][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-15 00:02:55.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.546][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:02:55.548][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-15 00:02:55.552][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-15 00:02:55.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.556][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.557][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-15 00:02:55.558][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-15 00:02:55.559][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-15 00:02:55.561][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.564][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.567][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-15 00:02:55.570][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.573][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-15 00:02:55.575][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.577][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:55.580][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.582][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.584][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.586][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.588][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:02:55.590][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:55.592][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.594][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-15 00:02:55.596][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:55.598][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.602][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.605][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:02:55.605][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:02:55.605][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:02:55.605][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:02:55.605][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:02:55.608][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:55.610][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.614][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.616][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:55.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.623][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.625][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.627][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:55.630][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:55.632][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.634][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.637][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-15 00:02:55.641][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.643][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:02:55.646][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.648][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:55.651][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.654][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.657][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.659][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.662][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:02:55.664][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:55.667][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.670][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-15 00:02:55.672][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:55.674][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.676][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.679][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:02:55.679][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:02:55.679][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:02:55.679][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:02:55.679][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:02:55.681][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:55.683][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.685][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.687][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:55.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.693][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.695][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.697][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:55.700][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:55.702][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.704][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.706][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-15 00:02:55.709][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.712][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-15 00:02:55.714][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.716][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:55.718][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.720][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.722][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.725][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.727][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:02:55.729][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:55.731][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.733][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-15 00:02:55.735][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:55.737][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.738][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.740][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.741][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:55.744][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.745][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.748][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:55.750][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.754][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.756][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.758][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:55.761][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:55.763][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.765][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.767][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-15 00:02:55.770][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.773][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:02:55.775][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.778][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:55.780][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.782][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.784][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.787][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.789][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:02:55.791][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:55.794][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.796][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-15 00:02:55.798][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:55.801][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.803][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:55.805][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.807][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:02:55.810][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.812][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.813][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:55.815][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:55.817][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:55.819][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:55.822][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.824][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:55.825][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:55.828][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:55.830][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:02:55.870][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:02:55.873][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.875][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.877][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.881][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.885][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[2025-08-15 00:02:55.888][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.892][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.900][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.909][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.913][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[2025-08-15 00:02:55.914][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.916][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.918][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.920][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.924][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.928][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.932][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[2025-08-15 00:02:55.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.942][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[2025-08-15 00:02:55.944][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.948][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.952][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.954][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.963][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.DEBUG[2025-08-15 00:02:55.965][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.969][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.983][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[2025-08-15 00:02:55.985][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:55.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:55.993][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:55.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:55.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:55.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.009][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[2025-08-15 00:02:56.011][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.018][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.020][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.028][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.037][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.039][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-15 00:02:56.042][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-15 00:02:56.045][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-15 00:02:56.048][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-15 00:02:56.051][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:02:56.054][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-15 00:02:56.057][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-15 00:02:56.060][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-15 00:02:56.063][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-15 00:02:56.066][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-15 00:02:56.069][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:02:56.071][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-15 00:02:56.074][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-15 00:02:56.077][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-15 00:02:56.080][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-15 00:02:56.083][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-15 00:02:56.086][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-15 00:02:56.089][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-15 00:02:56.092][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:02:56.095][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-15 00:02:56.097][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-15 00:02:56.099][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-15 00:02:56.102][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-15 00:02:56.105][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-15 00:02:56.108][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-15 00:02:56.111][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-15 00:02:56.114][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-15 00:02:56.116][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-15 00:02:56.118][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-15 00:02:56.120][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-15 00:02:56.122][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-15 00:02:56.125][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-15 00:02:56.128][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-15 00:02:56.131][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-15 00:02:56.134][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-15 00:02:56.138][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-15 00:02:56.141][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-15 00:02:56.144][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-15 00:02:56.147][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-15 00:02:56.150][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-15 00:02:56.153][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-15 00:02:56.156][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-15 00:02:56.159][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-15 00:02:56.162][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-15 00:02:56.166][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-15 00:02:56.169][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-15 00:02:56.172][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-15 00:02:56.175][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-15 00:02:56.178][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-15 00:02:56.181][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-15 00:02:56.183][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-15 00:02:56.186][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-15 00:02:56.189][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-15 00:02:56.193][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-15 00:02:56.196][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-15 00:02:56.198][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-15 00:02:56.201][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-15 00:02:56.204][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-15 00:02:56.207][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-15 00:02:56.210][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-15 00:02:56.213][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-15 00:02:56.216][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-15 00:02:56.219][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-15 00:02:56.222][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-15 00:02:56.224][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-15 00:02:56.227][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-15 00:02:56.230][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:02:56.232][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:02:56.235][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-15 00:02:56.238][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-15 00:02:56.241][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-15 00:02:56.243][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-15 00:02:56.246][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-15 00:02:56.249][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-15 00:02:56.252][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-15 00:02:56.255][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-15 00:02:56.258][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-15 00:02:56.261][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-15 00:02:56.264][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-15 00:02:56.267][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-15 00:02:56.270][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-15 00:02:56.273][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-15 00:02:56.276][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-15 00:02:56.279][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-15 00:02:56.283][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:02:56.285][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:02:56.287][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.289][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.294][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.299][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.303][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.308][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.337][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.341][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.369][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[2025-08-15 00:02:56.371][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.390][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.394][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.398][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[2025-08-15 00:02:56.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.402][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.412][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[2025-08-15 00:02:56.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.417][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.421][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.425][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.431][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.443][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.447][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.452][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.454][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.456][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.459][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.463][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[2025-08-15 00:02:56.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.481][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.490][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.492][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.494][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.495][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.497][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.501][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:56.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:02:56.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:56.506][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:56.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:56.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:56.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:56.514][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[2025-08-15 00:02:56.518][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-15 00:02:56.521][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-15 00:02:56.525][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:56.527][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-15 00:02:56.529][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:56.531][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:02:56.533][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:56.535][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:02:56.537][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:56.539][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-15 00:02:56.542][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-15 00:02:56.544][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:02:56.546][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:56.548][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-15 00:02:56.550][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-15 00:02:56.552][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-15 00:02:56.554][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-15 00:02:56.556][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:02:56.556][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:02:56.556][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:02:56.558][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-15 00:02:56.560][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:56.562][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:56.564][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:02:56.566][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:02:56.568][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:02:56.570][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:02:56.572][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:02:56.572][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-15 00:02:56.574][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:02:56.576][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:02:56.578][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-15 00:02:56.580][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-15 00:02:56.580][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-15 00:02:56.582][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:02:56.585][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:02:56.588][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-15 00:02:56.591][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:02:56.594][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:02:56.596][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:02:56.602][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-15 00:02:56.605][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-15 00:02:56.607][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-15 00:02:56.611][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-15 00:02:56.613][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:02:56.615][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:02:56.618][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-15 00:02:56.620][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-15 00:02:56.623][biodb::testThat]
biodb.INFO [2025-08-15 00:02:56.625][biodb::testThat] Running test function test_chebi_convCasToChebi (" convCasToChebi() works. ").
biodb.INFO [2025-08-15 00:02:56.627][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:02:56.629][biodb::testThat]
biodb.DEBUG[2025-08-15 00:02:56.635][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-15 00:02:56.644][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:56.646][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:56.649][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.TRACE[2025-08-15 00:02:56.954][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl).
biodb.DEBUG[2025-08-15 00:02:57.351][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:57.355][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content"
biodb.TRACE[2025-08-15 00:02:57.362][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.request"
biodb.DEBUG[2025-08-15 00:02:57.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:02:57.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:57.379][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:57.383][private$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[2025-08-15 00:02:57.708][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[2025-08-15 00:02:57.997][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:02:58.000][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content"
biodb.TRACE[2025-08-15 00:02:58.005][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.request"
biodb.DEBUG[2025-08-15 00:02:58.009][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:02:58.010][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:02:58.011][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:02:59.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:02:59.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:02:59.320][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:02:59.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:02:59.326][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[2025-08-15 00:02:59.332][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:02:59.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:02:59.338][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:02:59.818][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY%20NUMBERS&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:03:00.117][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:03:00.121][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content"
biodb.TRACE[2025-08-15 00:03:00.127][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.request"
biodb.DEBUG[2025-08-15 00:03:00.132][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.134][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.136][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.152][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.181][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.183][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.197][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.210][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:00.216][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:00.219][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-15 00:03:00.222][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:00.226][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-15 00:03:00.230][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.247][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.251][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.255][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:00.261][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:00.264][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-15 00:03:00.267][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:00.272][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-15 00:03:00.275][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.277][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.279][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.291][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.293][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.295][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.297][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.300][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.301][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.303][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.313][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.317][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.326][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=51-41-2&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:00.332][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:00.335][cch$loadFileContent] Trying to load 1 files from cache: [1]: "0e2b277bfac878e1dcf7dc3f91acb8d3".
biodb.TRACE[2025-08-15 00:03:00.338][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:00.342][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/0e2b277bfac878e1dcf7dc3f91acb8d3.content".
biodb.DEBUG[2025-08-15 00:03:00.345][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.347][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.361][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.365][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.367][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.371][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=87605-72-9&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:00.377][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:00.380][cch$loadFileContent] Trying to load 1 files from cache: [1]: "b767b3e02c49727a1749efea3e381744".
biodb.TRACE[2025-08-15 00:03:00.383][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:00.387][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/b767b3e02c49727a1749efea3e381744.content".
biodb.DEBUG[2025-08-15 00:03:00.391][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:00.393][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:00.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:00.407][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:00.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:00.412][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:00.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:00.416][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=14215-68-0&searchCategory=REGISTRY NUMBERS&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:00.421][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:03:00.423][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:03:00.427][private$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[2025-08-15 00:03:00.739][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[2025-08-15 00:03:01.042][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:03:01.047][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.content"
biodb.TRACE[2025-08-15 00:03:01.056][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/70e3912746e7e39b39fbbffe6c90b502.request"
biodb.DEBUG[2025-08-15 00:03:01.061][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:01.063][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:01.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:01.077][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:01.079][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:01.082][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:01.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-15 00:03:01.362][biodb::testThat]
biodb.INFO [2025-08-15 00:03:01.364][biodb::testThat] Running test function test_chebi_convInchiToChebi (" convInchiToChebi() works. ").
biodb.INFO [2025-08-15 00:03:01.366][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:03:01.368][biodb::testThat]
biodb.DEBUG[2025-08-15 00:03:01.375][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[2025-08-15 00:03:01.381][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:03:01.384][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:03:01.388][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:03:01.727][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=InChI%3D1S%2FC15H24%2Fc1-9%282%2911-7-8-15%284%2912-6-5-10%283%2914%2815%2913%2811%2912%2Fh5%2C9%2C11-14H%2C6-8H2%2C1-4H3%2Ft11%3F%2C12%3F%2C13%3F%2C14%3F%2C15-%2Fm0%2Fs1&searchCategory=INCHI%2FINCHI%20KEY&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:03:02.033][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:03:02.036][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.content"
biodb.TRACE[2025-08-15 00:03:02.044][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/64007787a4f3864bb479683766386808.request"
biodb.DEBUG[2025-08-15 00:03:02.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:02.050][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:02.052][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:02.063][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:02.066][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:02.068][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.078][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=VLXDPFLIRFYIME-MWHZVNNOSA-N&searchCategory=INCHI/INCHI KEY&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:02.083][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:03:02.085][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:03:02.087][private$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[2025-08-15 00:03:02.382][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[2025-08-15 00:03:02.691][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:03:02.696][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.content"
biodb.TRACE[2025-08-15 00:03:02.701][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/7547b08b3ebd50447d61026ab0af8d63.request"
biodb.DEBUG[2025-08-15 00:03:02.705][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:02.706][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:02.708][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:02.716][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:02.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:02.719][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.721][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.INFO [2025-08-15 00:03:02.734][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-15 00:03:02.737][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-15 00:03:02.739][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-15 00:03:02.741][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-15 00:03:02.743][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:02.745][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:02.747][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:02.749][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:02.751][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.753][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.INFO [2025-08-15 00:03:02.761][biodb::testContext]
biodb.INFO [2025-08-15 00:03:02.763][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:03:02.765][biodb::testContext] Test context - Test web services
biodb.INFO [2025-08-15 00:03:02.768][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:03:02.769][biodb::testContext]
biodb.INFO [2025-08-15 00:03:02.772][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:03:02.775][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-15 00:03:02.781][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:03:02.782][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-15 00:03:02.784][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-15 00:03:02.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.788][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-15 00:03:02.790][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-15 00:03:02.791][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.793][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[2025-08-15 00:03:02.795][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-15 00:03:02.797][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-15 00:03:02.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.805][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-15 00:03:02.807][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-15 00:03:02.809][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-15 00:03:02.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.817][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-15 00:03:02.819][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-15 00:03:02.821][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-15 00:03:02.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.829][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-15 00:03:02.831][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-15 00:03:02.833][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.834][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.836][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[2025-08-15 00:03:02.838][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-15 00:03:02.840][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-15 00:03:02.842][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-15 00:03:02.844][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.846][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.850][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-15 00:03:02.852][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-15 00:03:02.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.859][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-15 00:03:02.861][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-15 00:03:02.864][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-15 00:03:02.865][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.869][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.871][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:03:02.873][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-15 00:03:02.875][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-15 00:03:02.877][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-15 00:03:02.879][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-15 00:03:02.881][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-15 00:03:02.883][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.888][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-15 00:03:02.891][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-15 00:03:02.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.896][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.898][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-15 00:03:02.900][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-15 00:03:02.902][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.906][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[2025-08-15 00:03:02.908][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-15 00:03:02.910][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-15 00:03:02.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.914][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.918][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-15 00:03:02.920][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-15 00:03:02.922][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.926][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.928][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-15 00:03:02.930][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-15 00:03:02.932][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.935][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.955][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:03:02.957][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-15 00:03:02.961][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-15 00:03:02.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.965][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.969][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-15 00:03:02.971][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-15 00:03:02.973][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-15 00:03:02.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:02.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:02.980][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:02.982][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-15 00:03:02.985][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:02.987][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2025-08-15 00:03:02.988][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:02.990][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:02.992][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:02.993][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:02.995][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:02.996][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:02.998][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:03:02.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:03.000][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.002][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-15 00:03:03.003][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:03.004][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.006][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.008][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:03:03.008][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:03:03.008][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:03:03.008][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:03:03.008][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:03:03.009][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:03.011][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.012][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.013][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:03.015][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.016][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.017][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.018][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.020][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:03.021][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:03.022][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.024][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.025][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-15 00:03:03.027][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.029][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:03:03.031][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.033][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:03.034][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.035][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.037][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.038][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.039][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:03:03.041][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:03.043][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.045][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-15 00:03:03.047][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:03.049][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.051][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.053][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:03:03.053][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:03:03.053][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:03:03.053][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:03:03.053][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:03:03.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:03.057][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.059][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.061][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:03.063][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.065][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.067][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.069][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.071][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:03.072][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:03.074][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.075][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.077][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-15 00:03:03.080][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.082][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2025-08-15 00:03:03.084][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.086][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:03.088][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.089][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.091][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.093][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.094][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:03:03.096][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:03.097][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.099][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-15 00:03:03.100][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:03.102][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.104][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.106][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.108][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:03.109][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.111][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.112][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:03.113][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.115][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.116][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.117][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.119][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:03.120][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:03.121][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.123][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.125][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-15 00:03:03.127][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.129][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:03:03.132][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.133][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:03.135][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.136][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.137][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.139][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.141][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:03:03.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:03.145][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.147][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-15 00:03:03.149][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:03.151][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.153][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.155][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.157][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:03.159][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.162][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.164][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:03.166][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.168][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.170][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.173][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.175][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:03.178][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:03.180][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.182][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:03.185][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:03:03.187][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.189][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[2025-08-15 00:03:03.191][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.197][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.199][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.211][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.245][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.249][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.251][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.255][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.264][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.270][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.284][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.291][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.295][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.299][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.301][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.305][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.318][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.326][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.338][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.351][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.353][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.359][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-15 00:03:03.362][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-15 00:03:03.365][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-15 00:03:03.367][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-15 00:03:03.370][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:03:03.373][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-15 00:03:03.376][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-15 00:03:03.379][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-15 00:03:03.382][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-15 00:03:03.384][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-15 00:03:03.387][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:03:03.390][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-15 00:03:03.393][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-15 00:03:03.396][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-15 00:03:03.399][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-15 00:03:03.402][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-15 00:03:03.405][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-15 00:03:03.408][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-15 00:03:03.411][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:03:03.414][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-15 00:03:03.415][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-15 00:03:03.417][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-15 00:03:03.419][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-15 00:03:03.421][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-15 00:03:03.423][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-15 00:03:03.425][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-15 00:03:03.427][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-15 00:03:03.428][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-15 00:03:03.430][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-15 00:03:03.432][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-15 00:03:03.434][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-15 00:03:03.436][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-15 00:03:03.438][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-15 00:03:03.441][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-15 00:03:03.444][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-15 00:03:03.447][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-15 00:03:03.449][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-15 00:03:03.452][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-15 00:03:03.455][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-15 00:03:03.458][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-15 00:03:03.461][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-15 00:03:03.464][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-15 00:03:03.467][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-15 00:03:03.469][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-15 00:03:03.472][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-15 00:03:03.475][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-15 00:03:03.478][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-15 00:03:03.481][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-15 00:03:03.484][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-15 00:03:03.487][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-15 00:03:03.490][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-15 00:03:03.492][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-15 00:03:03.495][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-15 00:03:03.498][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-15 00:03:03.500][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-15 00:03:03.502][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-15 00:03:03.504][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-15 00:03:03.506][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-15 00:03:03.508][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-15 00:03:03.510][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-15 00:03:03.512][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-15 00:03:03.514][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-15 00:03:03.516][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-15 00:03:03.518][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-15 00:03:03.519][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-15 00:03:03.522][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-15 00:03:03.523][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:03:03.525][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:03:03.527][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-15 00:03:03.529][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-15 00:03:03.530][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-15 00:03:03.532][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-15 00:03:03.534][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-15 00:03:03.536][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-15 00:03:03.539][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-15 00:03:03.542][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-15 00:03:03.545][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-15 00:03:03.548][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-15 00:03:03.550][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-15 00:03:03.552][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-15 00:03:03.554][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-15 00:03:03.556][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-15 00:03:03.558][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-15 00:03:03.560][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-15 00:03:03.563][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:03:03.565][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:03:03.567][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.569][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.571][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.573][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.575][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.577][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.579][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.581][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.582][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.584][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.586][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.592][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.596][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.600][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.602][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.606][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.608][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.614][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.617][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.618][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.624][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.634][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.642][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.649][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.651][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.654][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.667][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.671][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.675][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.685][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.689][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.692][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.DEBUG[2025-08-15 00:03:03.694][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.698][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.699][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.710][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.712][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.714][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.717][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.736][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.739][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.742][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[2025-08-15 00:03:03.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.748][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.753][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[2025-08-15 00:03:03.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.760][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.762][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.767][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.776][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.780][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.781][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:03.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:03.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:03.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:03.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:03.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:03.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:03.800][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[2025-08-15 00:03:03.805][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-15 00:03:03.808][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-15 00:03:03.811][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.813][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.815][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.817][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:03.819][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.823][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.825][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-15 00:03:03.827][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-15 00:03:03.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:03.831][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.833][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-15 00:03:03.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-15 00:03:03.838][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-15 00:03:03.840][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:03.842][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:03:03.842][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:03:03.842][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:03:03.844][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-15 00:03:03.846][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.848][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.850][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:03.852][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:03.854][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:03.856][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:03.858][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:03:03.858][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-15 00:03:03.860][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:03.862][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:03.863][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:03.865][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-15 00:03:03.865][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-15 00:03:03.868][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:03:03.871][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:03:03.874][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-15 00:03:03.877][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:03:03.880][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:03:03.882][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:03:03.886][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-15 00:03:03.887][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-15 00:03:03.888][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-15 00:03:03.890][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-15 00:03:03.892][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:03:03.893][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:03:03.895][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-15 00:03:03.898][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-15 00:03:03.901][biodb::testThat]
biodb.INFO [2025-08-15 00:03:03.903][biodb::testThat] Running test function test.chebi.wsGetLiteEntity (" Web service getLiteEntity works fine. ").
biodb.INFO [2025-08-15 00:03:03.905][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:03:03.907][biodb::testThat]
biodb.DEBUG[2025-08-15 00:03:03.912][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-15 00:03:03.919][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:03.923][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-15 00:03:03.926][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:03.930][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-15 00:03:03.937][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[2025-08-15 00:03:03.944][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:03:03.947][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:03:03.950][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL".
biodb.TRACE[2025-08-15 00:03:04.246][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI%20ID&maximumResults=10&starsCategory=ALL).
biodb.DEBUG[2025-08-15 00:03:04.561][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:03:04.565][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content"
biodb.TRACE[2025-08-15 00:03:04.574][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.request"
biodb.INFO [2025-08-15 00:03:04.592][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-15 00:03:04.595][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-15 00:03:04.597][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-15 00:03:04.599][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-15 00:03:04.601][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:04.603][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:04.605][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.607][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.609][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2025-08-15 00:03:04.619][biodb::testContext]
biodb.INFO [2025-08-15 00:03:04.622][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:03:04.624][biodb::testContext] Test context - Non regression tests
biodb.INFO [2025-08-15 00:03:04.626][biodb::testContext] ********************************************************************************
biodb.INFO [2025-08-15 00:03:04.627][biodb::testContext]
biodb.INFO [2025-08-15 00:03:04.632][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:03:04.635][self$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2025-08-15 00:03:04.640][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:03:04.642][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2025-08-15 00:03:04.643][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2025-08-15 00:03:04.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.647][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.648][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2025-08-15 00:03:04.649][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2025-08-15 00:03:04.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.654][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2025-08-15 00:03:04.655][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2025-08-15 00:03:04.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.660][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2025-08-15 00:03:04.661][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2025-08-15 00:03:04.663][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2025-08-15 00:03:04.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.665][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.666][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.668][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2025-08-15 00:03:04.670][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2025-08-15 00:03:04.672][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2025-08-15 00:03:04.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.679][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2025-08-15 00:03:04.681][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2025-08-15 00:03:04.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.689][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2025-08-15 00:03:04.691][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2025-08-15 00:03:04.693][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2025-08-15 00:03:04.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.700][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2025-08-15 00:03:04.702][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2025-08-15 00:03:04.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.709][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2025-08-15 00:03:04.710][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2025-08-15 00:03:04.711][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2025-08-15 00:03:04.712][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.715][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[2025-08-15 00:03:04.716][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:03:04.717][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2025-08-15 00:03:04.719][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2025-08-15 00:03:04.720][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2025-08-15 00:03:04.721][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2025-08-15 00:03:04.722][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2025-08-15 00:03:04.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.727][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2025-08-15 00:03:04.728][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2025-08-15 00:03:04.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.731][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.732][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[2025-08-15 00:03:04.733][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2025-08-15 00:03:04.734][self$set] Set key entries.sep to "|".
biodb.DEBUG[2025-08-15 00:03:04.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.739][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2025-08-15 00:03:04.740][self$set] Set key offline to FALSE.
biodb.DEBUG[2025-08-15 00:03:04.741][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.745][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2025-08-15 00:03:04.746][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2025-08-15 00:03:04.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.751][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2025-08-15 00:03:04.752][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2025-08-15 00:03:04.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.756][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[2025-08-15 00:03:04.757][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2025-08-15 00:03:04.758][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2025-08-15 00:03:04.762][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2025-08-15 00:03:04.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.767][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2025-08-15 00:03:04.768][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2025-08-15 00:03:04.770][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2025-08-15 00:03:04.771][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.775][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2025-08-15 00:03:04.777][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.778][self$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[2025-08-15 00:03:04.779][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.781][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:04.782][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.783][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.784][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.786][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.787][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:03:04.788][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:04.790][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.791][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2025-08-15 00:03:04.792][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:04.794][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.795][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.796][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:03:04.796][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:03:04.796][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:03:04.796][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:03:04.796][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:03:04.798][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:04.800][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.801][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.802][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:04.803][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.805][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.806][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.807][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.808][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:04.810][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:04.811][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.812][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.814][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2025-08-15 00:03:04.816][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.817][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:03:04.818][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.820][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:04.821][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.822][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.824][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.825][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.826][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:03:04.828][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:04.829][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.830][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2025-08-15 00:03:04.832][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:04.833][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.835][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.837][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:03:04.837][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:03:04.837][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:03:04.837][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2025-08-15 00:03:04.837][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2025-08-15 00:03:04.838][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:04.839][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.840][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.842][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:04.843][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.844][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.845][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.847][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.848][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:04.849][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:04.850][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.852][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.853][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2025-08-15 00:03:04.855][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.857][self$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[2025-08-15 00:03:04.858][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.860][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:04.861][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.862][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.864][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.865][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.866][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2025-08-15 00:03:04.868][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:04.869][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.870][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2025-08-15 00:03:04.871][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:04.873][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.874][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.875][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.877][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:04.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.880][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:04.881][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.883][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.884][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.885][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.886][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:04.888][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:04.889][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.890][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.892][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2025-08-15 00:03:04.894][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.895][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2025-08-15 00:03:04.896][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.897][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:04.899][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.900][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.901][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.902][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.904][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2025-08-15 00:03:04.905][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:04.906][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.908][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2025-08-15 00:03:04.910][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:04.920][self$setPropertyValue] Setting property "parsing.expr" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.921][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:04.923][self$setPropertyValue] Setting property "searchable.fields" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.924][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2025-08-15 00:03:04.925][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.926][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.927][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:04.929][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:04.930][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:04.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:04.932][self$setPropertyValue] Setting property "urls" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.933][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:04.934][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:04.936][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:04.937][self$setPropertyValue] Setting property "xml.ns" to "<NULL>".
biodb.DEBUG[2025-08-15 00:03:04.939][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:03:04.941][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.943][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[2025-08-15 00:03:04.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.949][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.963][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.DEBUG[2025-08-15 00:03:04.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.968][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:04.983][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.987][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:04.991][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[2025-08-15 00:03:04.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:04.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:04.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:04.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.011][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.017][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.023][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.027][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.030][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[2025-08-15 00:03:05.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.034][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.036][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.040][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.042][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.048][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.050][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.051][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.053][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.060][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.068][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.070][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.078][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[2025-08-15 00:03:05.080][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.088][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.098][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[2025-08-15 00:03:05.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.106][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.109][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2025-08-15 00:03:05.111][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2025-08-15 00:03:05.114][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2025-08-15 00:03:05.117][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2025-08-15 00:03:05.119][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:03:05.122][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2025-08-15 00:03:05.125][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2025-08-15 00:03:05.127][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2025-08-15 00:03:05.130][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2025-08-15 00:03:05.133][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2025-08-15 00:03:05.135][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:03:05.138][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2025-08-15 00:03:05.141][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2025-08-15 00:03:05.144][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2025-08-15 00:03:05.147][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2025-08-15 00:03:05.150][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2025-08-15 00:03:05.153][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2025-08-15 00:03:05.156][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2025-08-15 00:03:05.159][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:03:05.161][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2025-08-15 00:03:05.164][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2025-08-15 00:03:05.167][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2025-08-15 00:03:05.170][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2025-08-15 00:03:05.173][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2025-08-15 00:03:05.176][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2025-08-15 00:03:05.179][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2025-08-15 00:03:05.182][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2025-08-15 00:03:05.185][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2025-08-15 00:03:05.188][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2025-08-15 00:03:05.191][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2025-08-15 00:03:05.194][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2025-08-15 00:03:05.197][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2025-08-15 00:03:05.200][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2025-08-15 00:03:05.203][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2025-08-15 00:03:05.206][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2025-08-15 00:03:05.209][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2025-08-15 00:03:05.211][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2025-08-15 00:03:05.214][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2025-08-15 00:03:05.217][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2025-08-15 00:03:05.220][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2025-08-15 00:03:05.222][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2025-08-15 00:03:05.225][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2025-08-15 00:03:05.228][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2025-08-15 00:03:05.231][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2025-08-15 00:03:05.233][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2025-08-15 00:03:05.236][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2025-08-15 00:03:05.239][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2025-08-15 00:03:05.242][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2025-08-15 00:03:05.244][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2025-08-15 00:03:05.247][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2025-08-15 00:03:05.250][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2025-08-15 00:03:05.253][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2025-08-15 00:03:05.255][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2025-08-15 00:03:05.258][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2025-08-15 00:03:05.261][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2025-08-15 00:03:05.264][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2025-08-15 00:03:05.266][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2025-08-15 00:03:05.268][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2025-08-15 00:03:05.270][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2025-08-15 00:03:05.272][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2025-08-15 00:03:05.274][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2025-08-15 00:03:05.275][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2025-08-15 00:03:05.277][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2025-08-15 00:03:05.279][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2025-08-15 00:03:05.281][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2025-08-15 00:03:05.282][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2025-08-15 00:03:05.284][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:03:05.286][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:03:05.287][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2025-08-15 00:03:05.289][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2025-08-15 00:03:05.291][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2025-08-15 00:03:05.292][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2025-08-15 00:03:05.294][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2025-08-15 00:03:05.296][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2025-08-15 00:03:05.297][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2025-08-15 00:03:05.301][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2025-08-15 00:03:05.302][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2025-08-15 00:03:05.304][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2025-08-15 00:03:05.307][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2025-08-15 00:03:05.309][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2025-08-15 00:03:05.311][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2025-08-15 00:03:05.312][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2025-08-15 00:03:05.315][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2025-08-15 00:03:05.318][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2025-08-15 00:03:05.321][initialize] This is biodb version 1.16.0.
biodb.DEBUG[2025-08-15 00:03:05.324][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2025-08-15 00:03:05.326][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.330][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.331][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[2025-08-15 00:03:05.333][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.337][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.350][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.354][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.363][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.369][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.371][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.376][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.DEBUG[2025-08-15 00:03:05.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.380][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.385][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[2025-08-15 00:03:05.386][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.387][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.393][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[2025-08-15 00:03:05.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.397][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.402][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[2025-08-15 00:03:05.403][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.406][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.408][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.412][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.413][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.414][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.418][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.425][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.428][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.434][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.441][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.442][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.444][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.445][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.446][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.453][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.456][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[2025-08-15 00:03:05.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.460][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.465][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.468][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.470][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.472][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[2025-08-15 00:03:05.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2025-08-15 00:03:05.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.486][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.493][biodb$loadDefinitions] Load definitions from file "E:/biocbuild/bbs-3.21-bioc/R/library/biodbChebi/definitions.yml".
biodb.DEBUG[2025-08-15 00:03:05.495][self$getDbsInfo()$define] Define connector chebi.
biodb.DEBUG[2025-08-15 00:03:05.497][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:05.499][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2025-08-15 00:03:05.500][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:05.501][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2025-08-15 00:03:05.502][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:05.504][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2025-08-15 00:03:05.505][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:05.506][self$setPropertyValue] Setting property "entry.content.encoding" to "UTF-8".
biodb.DEBUG[2025-08-15 00:03:05.507][self$setPropertyValue] Setting property "entry.content.type" to "xml".
biodb.DEBUG[2025-08-15 00:03:05.509][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2025-08-15 00:03:05.510][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:05.511][self$setPropertyValue] Setting property "name" to "ChEBI".
biodb.DEBUG[2025-08-15 00:03:05.513][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "substring-after(//chebi:return/chebi:chebiId,'CHEBI:')".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:charge".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:Formulae/chebi:source[text()='ChEBI']/../chebi:data", "(//chebi:Formulae/chebi:data)[1]")".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchi".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:inchiKey".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:DatabaseLinks/chebi:type[text()='KEGG COMPOUND accession']/../chebi:data".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:mass".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:monoisotopicMass".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "c("//chebi:chebiAsciiName", "//chebi:Synonyms/chebi:data")".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:entityStar".
biodb.DEBUG[2025-08-15 00:03:05.515][self$setPropertyValue] Setting property "parsing.expr" to "//chebi:return/chebi:smiles".
biodb.DEBUG[2025-08-15 00:03:05.517][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2025-08-15 00:03:05.519][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2025-08-15 00:03:05.519][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2025-08-15 00:03:05.519][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2025-08-15 00:03:05.521][self$setPropertyValue] Setting property "scheduler.n" to "3".
biodb.DEBUG[2025-08-15 00:03:05.523][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:05.525][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:05.527][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2025-08-15 00:03:05.528][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2025-08-15 00:03:05.530][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2025-08-15 00:03:05.532][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2025-08-15 00:03:05.534][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:03:05.534][self$setPropertyValue] Setting property "urls" to "https://www.ebi.ac.uk/webservices/chebi/2.0/".
biodb.DEBUG[2025-08-15 00:03:05.535][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2025-08-15 00:03:05.537][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2025-08-15 00:03:05.538][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2025-08-15 00:03:05.539][self$setPropertyValue] Setting property "xml.ns" to "https://www.ebi.ac.uk/webservices/chebi".
biodb.DEBUG[2025-08-15 00:03:05.539][self$setPropertyValue] Setting property "xml.ns" to "http://www.w3.org/2001/XMLSchema".
biodb.DEBUG[2025-08-15 00:03:05.541][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2025-08-15 00:03:05.543][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2025-08-15 00:03:05.545][self$getEntryFields()$define] Define field n_stars.
biodb.DEBUG[2025-08-15 00:03:05.546][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2025-08-15 00:03:05.548][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2025-08-15 00:03:05.550][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2025-08-15 00:03:05.561][super$initialize] Initialize connector chebi.
biodb.DEBUG[2025-08-15 00:03:05.563][super$initialize] Register connector chebi with the request scheduler
biodb.DEBUG[2025-08-15 00:03:05.564][private$bdb$getRequestScheduler()$re ...] Register connector chebi.
biodb.DEBUG[2025-08-15 00:03:05.566][private$addConnectorRules] Create new rule for URL "www.ebi.ac.uk" of connector "chebi".
biodb.DEBUG[2025-08-15 00:03:05.568][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:03:05.569][self$setFrequency] t=1.000000, n=3.000000
biodb.DEBUG[2025-08-15 00:03:05.571][rule$addConnector] Connector "chebi" is already listed in rule "www.ebi.ac.uk".
biodb.DEBUG[2025-08-15 00:03:05.572][biodb$getFactory()$createConn] Creating new connector chebi for database class chebi .
biodb.INFO [2025-08-15 00:03:05.574][biodb::testThat]
biodb.INFO [2025-08-15 00:03:05.576][biodb::testThat] Running test function test.chebi.encoding.issue.in.xml (" ChEBI encoding issue in XML is handled. ").
biodb.INFO [2025-08-15 00:03:05.577][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2025-08-15 00:03:05.578][biodb::testThat]
biodb.DEBUG[2025-08-15 00:03:05.582][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/webservice?wsdl".
biodb.DEBUG[2025-08-15 00:03:05.587][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:05.588][cch$loadFileContent] Trying to load 1 files from cache: [1]: "1ad88a023c4ce2bc0629db4acebeee05".
biodb.TRACE[2025-08-15 00:03:05.590][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:05.593][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/1ad88a023c4ce2bc0629db4acebeee05.content".
biodb.DEBUG[2025-08-15 00:03:05.597][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getLiteEntity?search=2571&searchCategory=CHEBI ID&maximumResults=10&starsCategory=ALL".
biodb.DEBUG[2025-08-15 00:03:05.601][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2025-08-15 00:03:05.603][cch$loadFileContent] Trying to load 1 files from cache: [1]: "04c26672f8368e71348af4b34238160e".
biodb.TRACE[2025-08-15 00:03:05.605][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2025-08-15 00:03:05.607][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/04c26672f8368e71348af4b34238160e.content".
biodb.DEBUG[2025-08-15 00:03:05.612][private$loadEntries] Creating entries from ids [1]: "2571".
biodb.DEBUG[2025-08-15 00:03:05.613][conn$getEntryContent] Get ChEBI entry content(s) for 1 id(s)...
biodb.TRACE[2025-08-15 00:03:05.615][cch$loadFileContent] Trying to load 1 files from cache: [1]: "2571".
biodb.TRACE[2025-08-15 00:03:05.617][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2025-08-15 00:03:05.618][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2025-08-15 00:03:05.620][conn$getEntryContent] 0 ChEBI entry content(s) loaded from cache.
biodb.DEBUG[2025-08-15 00:03:05.621][conn$getEntryContent] 1 entry content(s) need to be fetched from ChEBI database "https://www.ebi.ac.uk/chebi/".
biodb.DEBUG[2025-08-15 00:03:05.622][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2025-08-15 00:03:05.624][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2025-08-15 00:03:05.627][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:05.628][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:05.629][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:05.636][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:05.638][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:05.639][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:05.640][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2025-08-15 00:03:05.643][scheduler$sendRequest] Getting content of get URL request "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.DEBUG[2025-08-15 00:03:05.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2025-08-15 00:03:05.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2025-08-15 00:03:05.649][private$doSendRequestOnce] Sent URL is "https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571".
biodb.TRACE[2025-08-15 00:03:11.316][getRCurlRequestResult] Using RCurl package for sending request (https://www.ebi.ac.uk/webservices/chebi/2.0/test/getCompleteEntity?chebiId=2571).
biodb.DEBUG[2025-08-15 00:03:11.907][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2025-08-15 00:03:11.911][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.content"
biodb.TRACE[2025-08-15 00:03:11.919][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/52df2611aa7f9f4c531cce8ac62e2fa0.request"
biodb.TRACE[2025-08-15 00:03:11.924][private$doSaveContentToFile] Saving to cache [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/chebi-0c5076ac2a43d16dbce503a44b09f649/2571.xml"
biodb.DEBUG[2025-08-15 00:03:11.927][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2025-08-15 00:03:11.930][self$createEntryFromContent] Creating ChEBI entries from 1 content(s).
biodb.DEBUG[2025-08-15 00:03:11.932][self$createEntryFromContent] Parsing 1 ChEBI entries.
biodb.DEBUG[2025-08-15 00:03:11.934][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2025-08-15 00:03:11.935][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:11.937][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:11.949][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:11.951][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:11.953][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:11.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2025-08-15 00:03:11.963][ef$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:11.965][ef$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:11.966][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:11.967][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:11.969][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:11.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:11.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:11.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:11.974][ef$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:03:11.976][ef$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:03:11.977][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:11.978][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:11.981][self$getBiodb()$getEntryFields()$get] Asked field names are: charge.
biodb.TRACE[2025-08-15 00:03:11.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: charge.
biodb.TRACE[2025-08-15 00:03:11.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:11.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:11.990][ef$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:03:11.992][ef$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:03:11.993][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:11.995][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:11.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2025-08-15 00:03:11.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2025-08-15 00:03:12.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.003][ef$get] Asked field names are: inchi.
biodb.TRACE[2025-08-15 00:03:12.005][ef$get] Realnames of fields are: inchi.
biodb.TRACE[2025-08-15 00:03:12.006][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.007][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.009][ef$get] Asked field names are: inchikey.
biodb.TRACE[2025-08-15 00:03:12.011][ef$get] Realnames of fields are: inchikey.
biodb.TRACE[2025-08-15 00:03:12.012][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.013][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.015][ef$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:03:12.016][ef$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:03:12.018][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.019][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.021][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:03:12.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2025-08-15 00:03:12.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.026][ef$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:03:12.028][ef$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:03:12.029][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.030][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.032][self$getBiodb()$getEntryFields()$get] Asked field names are: mass.
biodb.TRACE[2025-08-15 00:03:12.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2025-08-15 00:03:12.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.037][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:03:12.039][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:03:12.040][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.041][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.043][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:03:12.044][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2025-08-15 00:03:12.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.049][ef$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:03:12.051][ef$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:03:12.052][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.053][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.056][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2025-08-15 00:03:12.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2025-08-15 00:03:12.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.061][ef$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:03:12.063][ef$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:03:12.064][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.065][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.067][self$getBiodb()$getEntryFields()$get] Asked field names are: n_stars.
biodb.TRACE[2025-08-15 00:03:12.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: n.stars.
biodb.TRACE[2025-08-15 00:03:12.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.072][ef$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:03:12.074][ef$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:03:12.076][ef$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.078][ef$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.081][self$getBiodb()$getEntryFields()$get] Asked field names are: smiles.
biodb.TRACE[2025-08-15 00:03:12.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: smiles.
biodb.TRACE[2025-08-15 00:03:12.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.086][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:03:12.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:03:12.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.091][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:03:12.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:03:12.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.102][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2025-08-15 00:03:12.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2025-08-15 00:03:12.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.107][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.112][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.118][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.121][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.124][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.128][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.129][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.130][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.132][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.133][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2025-08-15 00:03:12.134][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2025-08-15 00:03:12.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2025-08-15 00:03:12.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2025-08-15 00:03:12.139][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2025-08-15 00:03:12.140][self$createEntryFromContent] Accession numbers: 2571.
biodb.INFO [2025-08-15 00:03:12.147][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2025-08-15 00:03:12.149][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector chebi from the request scheduler
biodb.INFO [2025-08-15 00:03:12.151][self$deleteConn] Connector "chebi" deleted.
biodb.DEBUG[2025-08-15 00:03:12.152][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2025-08-15 00:03:12.153][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2025-08-15 00:03:12.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2025-08-15 00:03:12.156][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2025-08-15 00:03:12.157][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2025-08-15 00:03:12.158][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2025-08-15 00:03:12.160][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".
[ FAIL 22 | WARN 0 | SKIP 0 | PASS 210 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
c(`15440` = "15440") %in% character(0) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(!!id %in% !!ids)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by name. ────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by name "squalene".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by name. ────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by name "squalene".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by name "squalene".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by name "squalene".
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.73 with mass field molecular.mass.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.73 with mass field molecular.mass.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.73 with mass field molecular.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.73 with mass field molecular.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.74 with mass field molecular.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.74 with mass field molecular.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.39125 with mass field monoisotopic.mass.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.39125 with mass field monoisotopic.mass.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.39125 with mass field monoisotopic.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.39125 with mass field monoisotopic.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
length(ids) > 0 is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.39126 with mass field monoisotopic.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(length(ids) > 0, msg)
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
id %in% ids is not TRUE
`actual`: FALSE
`expected`: TRUE
While searching for entry 15440 by mass 410.39126 with mass field monoisotopic.mass and by name
squalene.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id %in% ids, msg)
── Failure ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
c("mz", id.col) not identical to colnames(ret).
Lengths differ: 2 is not 1
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Error ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `if (file == "" || length(file) == 0) stop("empty or no content specified")`: missing value where TRUE/FALSE needed
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─conn$annotateMzValues(...)
4. └─self$searchForEntries(fieldsFilter, max.results = max.results)
5. └─private$doSearchForEntries(fields = fields, max.results = max.results)
6. └─private$searchByMass(...)
7. └─self$wsGetLiteEntity(...)
8. └─XML::xmlInternalTreeParse(results, asText = TRUE)
── Failure ('test_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
c("mz", id.col) not identical to colnames(ret).
Lengths differ: 2 is not 1
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_identical(c("mz", id.col), colnames(ret))
── Failure ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
id.col %in% colnames(ret) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<ChebiCnn>`, opt = `<named list>`)
3. └─testthat::expect_true(id.col %in% colnames(ret))
[ FAIL 22 | WARN 0 | SKIP 0 | PASS 210 ]
Error: Test failures
Execution halted
biodbChebi.Rcheck/biodbChebi-Ex.timings
| name | user | system | elapsed | |
| ChebiConn | 3.56 | 2.54 | 176.92 | |
| ChebiEntry | 0.47 | 0.02 | 0.49 | |