| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-04-17 11:36:35 -0400 (Wed, 17 Apr 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4676 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake" | 4414 |
| merida1 | macOS 12.7.1 Monterey | x86_64 | 4.3.3 (2024-02-29) -- "Angel Food Cake" | 4437 |
| 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 200/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.8.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the biodbLipidmaps package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.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: biodbLipidmaps |
| Version: 1.8.0 |
| Command: F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz |
| StartedAt: 2024-04-15 22:44:11 -0400 (Mon, 15 Apr 2024) |
| EndedAt: 2024-04-15 22:45:40 -0400 (Mon, 15 Apr 2024) |
| EllapsedTime: 89.8 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD check --no-multiarch --install=check:biodbLipidmaps.install-out.txt --library=F:\biocbuild\bbs-3.18-bioc\R\library --no-vignettes --timings biodbLipidmaps_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory 'F:/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck'
* using R version 4.3.3 (2024-02-29 ucrt)
* using platform: x86_64-w64-mingw32 (64-bit)
* R was compiled by
gcc.exe (GCC) 12.3.0
GNU Fortran (GCC) 12.3.0
* running under: Windows Server 2022 x64 (build 20348)
* using session charset: UTF-8
* using option '--no-vignettes'
* checking for file 'biodbLipidmaps/DESCRIPTION' ... OK
* this is package 'biodbLipidmaps' version '1.8.0'
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking whether package 'biodbLipidmaps' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in 'vignettes' ... OK
* checking examples ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
Running 'testthat.R'
ERROR
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 96 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in 'inst/doc' ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
'F:/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck/00check.log'
for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### F:\biocbuild\bbs-3.18-bioc\R\bin\R.exe CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library 'F:/biocbuild/bbs-3.18-bioc/R/library' * installing *source* package 'biodbLipidmaps' ... ** 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 (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R version 4.3.3 (2024-02-29 ucrt) -- "Angel Food Cake"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-04-15 22:45:18.904][biodb::testContext]
biodb.INFO [2024-04-15 22:45:18.907][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 22:45:18.908][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-04-15 22:45:18.910][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 22:45:18.911][biodb::testContext]
biodb.INFO [2024-04-15 22:45:18.918][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 22:45:18.921][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 22:45:18.930][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:18.932][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 22:45:18.933][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 22:45:18.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.937][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:18.938][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 22:45:18.958][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 22:45:18.959][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:18.963][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 22:45:18.965][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 22:45:18.966][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:18.970][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 22:45:18.971][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 22:45:18.972][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 22:45:18.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.976][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:18.977][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 22:45:18.979][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 22:45:18.980][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 22:45:18.981][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.984][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:18.985][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 22:45:18.987][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 22:45:18.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.991][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:18.992][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 22:45:18.993][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 22:45:18.995][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 22:45:18.996][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:18.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:18.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.000][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 22:45:19.001][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 22:45:19.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.007][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 22:45:19.009][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 22:45:19.010][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 22:45:19.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.014][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.016][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 22:45:19.017][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 22:45:19.018][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 22:45:19.020][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 22:45:19.021][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 22:45:19.023][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 22:45:19.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.027][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 22:45:19.029][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 22:45:19.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.034][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 22:45:19.035][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 22:45:19.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.040][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 22:45:19.042][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 22:45:19.043][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.044][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.045][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.047][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 22:45:19.048][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 22:45:19.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.053][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 22:45:19.055][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 22:45:19.056][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.059][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.060][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 22:45:19.061][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 22:45:19.065][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 22:45:19.066][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.069][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.070][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 22:45:19.071][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 22:45:19.073][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 22:45:19.074][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.081][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 22:45:19.115][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.132][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 22:45:19.134][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.135][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:19.136][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.138][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.139][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.141][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.142][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:19.143][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:19.145][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.147][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 22:45:19.148][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:19.149][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.151][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.152][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:19.152][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:19.152][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 22:45:19.152][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 22:45:19.152][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 22:45:19.153][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:19.155][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.156][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.157][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:19.165][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.166][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.168][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.169][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.170][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:19.171][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:19.172][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.173][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.175][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 22:45:19.177][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.178][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 22:45:19.179][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.180][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:19.181][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.182][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.184][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.185][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.186][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 22:45:19.187][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:19.188][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.190][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 22:45:19.191][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:19.192][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.193][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.194][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:19.194][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:19.194][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 22:45:19.194][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 22:45:19.194][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 22:45:19.196][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:19.197][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.198][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.199][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:19.200][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.203][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.205][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.207][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:19.209][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:19.210][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.212][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.214][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 22:45:19.217][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.219][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 22:45:19.221][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.223][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:19.225][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.227][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.229][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.230][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.232][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:19.234][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:19.236][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.238][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 22:45:19.240][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:19.242][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.244][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.245][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.247][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:19.249][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.253][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:19.255][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.256][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.258][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.260][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.262][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:19.263][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:19.265][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.267][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.269][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 22:45:19.272][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.274][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 22:45:19.276][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.278][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:19.280][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.282][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.283][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.286][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 22:45:19.287][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:19.288][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.290][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 22:45:19.291][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:19.292][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.293][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.294][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.295][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:19.297][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.298][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.299][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:19.300][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.301][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.302][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.303][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.304][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:19.306][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:19.307][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.308][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.312][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:19.313][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.314][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.315][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.323][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.325][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.326][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.331][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.337][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.348][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.349][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.354][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.358][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[2024-04-15 22:45:19.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.366][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.374][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.378][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.380][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.382][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.383][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.384][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.385][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.387][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.394][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.395][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.396][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.397][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.398][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.401][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.404][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.405][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.406][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.407][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.411][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 22:45:19.415][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 22:45:19.416][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 22:45:19.418][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 22:45:19.420][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 22:45:19.421][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 22:45:19.423][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 22:45:19.424][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 22:45:19.426][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 22:45:19.427][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 22:45:19.429][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 22:45:19.430][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 22:45:19.432][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 22:45:19.433][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 22:45:19.435][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 22:45:19.436][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 22:45:19.438][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 22:45:19.440][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 22:45:19.441][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 22:45:19.443][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 22:45:19.444][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 22:45:19.446][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 22:45:19.447][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 22:45:19.449][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 22:45:19.450][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 22:45:19.452][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 22:45:19.454][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 22:45:19.455][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 22:45:19.457][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 22:45:19.458][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 22:45:19.460][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 22:45:19.461][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 22:45:19.463][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 22:45:19.464][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 22:45:19.466][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 22:45:19.468][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 22:45:19.469][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 22:45:19.471][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 22:45:19.472][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 22:45:19.474][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 22:45:19.476][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 22:45:19.477][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 22:45:19.479][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 22:45:19.480][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 22:45:19.482][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 22:45:19.483][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 22:45:19.486][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 22:45:19.488][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 22:45:19.490][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 22:45:19.493][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 22:45:19.495][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 22:45:19.498][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 22:45:19.500][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 22:45:19.501][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 22:45:19.503][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 22:45:19.505][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 22:45:19.506][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 22:45:19.508][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 22:45:19.510][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 22:45:19.512][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 22:45:19.513][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 22:45:19.515][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 22:45:19.517][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 22:45:19.525][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 22:45:19.527][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 22:45:19.528][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 22:45:19.530][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 22:45:19.533][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 22:45:19.535][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 22:45:19.537][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 22:45:19.539][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 22:45:19.541][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 22:45:19.544][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 22:45:19.546][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 22:45:19.548][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 22:45:19.550][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 22:45:19.553][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 22:45:19.555][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 22:45:19.557][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 22:45:19.558][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 22:45:19.560][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 22:45:19.562][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 22:45:19.563][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 22:45:19.602][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 22:45:19.605][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 22:45:19.609][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:19.611][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.612][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.614][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.615][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.624][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.626][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.628][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.629][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.630][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.631][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.637][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.639][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.640][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.644][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.647][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.652][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.653][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.659][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.660][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.668][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.669][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.670][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.676][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.679][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.680][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.683][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.686][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.687][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.691][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.695][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.702][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.704][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.705][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.707][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.708][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.715][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.717][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.720][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.723][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.725][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.728][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.729][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.731][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.737][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.740][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.743][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.746][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.749][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.751][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:19.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.760][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.763][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:19.771][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 22:45:19.785][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:19.789][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.791][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.793][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.795][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:19.797][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.799][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.800][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.802][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.803][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:19.804][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:19.805][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.807][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 22:45:19.808][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 22:45:19.809][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 22:45:19.811][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:19.812][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:19.812][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:19.813][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:19.814][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.815][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.817][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:19.818][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:19.819][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:19.821][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:19.822][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 22:45:19.822][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 22:45:19.823][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:19.824][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:19.825][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:19.827][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:19.832][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 22:45:19.834][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 22:45:19.860][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:19.861][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 22:45:19.866][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:19.871][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 22:45:19.876][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 22:45:19.877][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 22:45:19.879][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 22:45:19.880][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 22:45:19.891][biodb::testThat]
biodb.INFO [2024-04-15 22:45:19.892][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-04-15 22:45:19.893][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:19.894][biodb::testThat]
biodb.TRACE[2024-04-15 22:45:19.901][loadFileContents] Loaded 1 files from cache: [1]: "F:/biocbuild/bbs-3.18-bioc/R/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-04-15 22:45:19.903][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 22:45:19.907][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 22:45:19.915][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:19.916][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:19.918][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:19.945][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:19.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:19.948][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:19.949][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:19.964][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:19.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:19.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:19.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:19.973][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:19.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:19.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:19.991][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:19.993][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-04-15 22:45:19.994][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-04-15 22:45:19.995][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:19.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:19.998][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 22:45:19.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-04-15 22:45:20.001][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.002][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.004][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-04-15 22:45:20.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-04-15 22:45:20.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.010][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.036][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.042][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.047][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.054][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 22:45:20.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.062][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-04-15 22:45:20.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.078][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.086][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.092][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.094][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.102][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 22:45:20.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.108][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.110][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-04-15 22:45:20.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.118][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.120][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.124][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.126][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.132][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.134][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-04-15 22:45:20.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.166][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.215][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.221][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.229][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.231][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.236][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.241][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.256][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.261][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.266][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.271][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.280][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:20.286][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-04-15 22:45:20.291][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 22:45:20.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 22:45:20.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.296][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-04-15 22:45:20.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-04-15 22:45:20.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.302][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-04-15 22:45:20.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-04-15 22:45:20.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.307][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-04-15 22:45:20.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-04-15 22:45:20.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.354][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.366][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.367][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.368][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.381][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.386][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.396][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.403][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.410][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:20.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.428][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.434][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.435][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.436][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.444][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.446][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.447][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.448][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.449][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.465][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.485][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.487][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.489][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.491][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.493][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.495][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.515][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.522][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.527][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.529][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.536][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.538][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.540][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.541][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.546][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.566][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.575][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.583][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.591][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.593][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.594][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.596][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.598][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.604][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.622][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.660][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.676][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.678][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.680][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.682][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.684][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.686][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.708][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.717][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.719][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.723][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.725][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.731][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.733][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.735][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.737][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.739][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.741][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.765][ef$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:20.767][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:20.769][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.771][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.783][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.785][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-04-15 22:45:20.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.789][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.801][ef$get] Asked field names are: formula.
biodb.TRACE[2024-04-15 22:45:20.803][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-04-15 22:45:20.805][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.807][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.818][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.821][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:20.823][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.825][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.836][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:20.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:20.841][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.843][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:20.854][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.857][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-04-15 22:45:20.859][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:20.861][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 22:45:20.881][biodb::testThat]
biodb.INFO [2024-04-15 22:45:20.883][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-04-15 22:45:20.885][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:20.887][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:20.910][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-04-15 22:45:20.920][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 22:45:20.930][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-04-15 22:45:20.932][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:20.937][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-04-15 22:45:20.940][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 22:45:20.978][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 22:45:20.981][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 22:45:20.984][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:20.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:20.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:20.996][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:20.998][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:20.999][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:21.000][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:21.003][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:21.005][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:21.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.009][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:21.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:21.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:21.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:21.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:21.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:21.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:21.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:21.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.036][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:21.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:21.040][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.042][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:21.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:21.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:21.050][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:21.052][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:21.053][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:21.055][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-04-15 22:45:21.056][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-15 22:45:21.080][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.081][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-04-15 22:45:21.083][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:21.084][biodb::testThat]
biodb.TRACE[2024-04-15 22:45:21.087][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:21.089][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:21.090][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:21.091][ef$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:21.093][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.INFO [2024-04-15 22:45:21.365][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.367][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-04-15 22:45:21.369][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:21.371][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.424][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.425][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-04-15 22:45:21.426][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:21.428][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.512][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.514][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-04-15 22:45:21.515][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:21.517][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.535][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.537][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-04-15 22:45:21.538][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:21.539][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.551][biodb::testThat]
biodb.INFO [2024-04-15 22:45:21.553][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-04-15 22:45:21.554][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:21.555][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:21.561][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-04-15 22:45:22.387][getUrlContent] Use base::url() for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-04-15 22:45:23.231][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.232][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-04-15 22:45:23.234][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.235][biodb::testThat]
biodb.TRACE[2024-04-15 22:45:23.256][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:23.258][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:23.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.261][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.262][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:23.264][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:23.265][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.267][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 22:45:23.270][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.271][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-04-15 22:45:23.272][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.273][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.331][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.333][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-04-15 22:45:23.334][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.335][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.367][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.369][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-04-15 22:45:23.371][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.372][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.393][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.395][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-04-15 22:45:23.396][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.398][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.420][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.421][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-04-15 22:45:23.422][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.423][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:23.426][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-04-15 22:45:23.472][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-04-15 22:45:23.489][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-04-15 22:45:23.491][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:23.496][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv".
biodb.DEBUG[2024-04-15 22:45:23.499][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 22:45:23.501][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-04-15 22:45:23.503][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 22:45:23.506][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:23.508][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:23.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:23.518][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:23.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:23.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:23.522][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:23.524][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.530][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.535][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.540][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.545][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.550][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.552][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.555][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.560][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:23.565][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-04-15 22:45:23.566][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-04-15 22:45:23.586][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.588][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-04-15 22:45:23.589][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.590][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:23.603][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-04-15 22:45:23.605][private$loadEntries] Creating entries from ids [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.DEBUG[2024-04-15 22:45:23.606][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 3 id(s)...
biodb.TRACE[2024-04-15 22:45:23.608][cch$loadFileContent] Trying to load 3 files from cache: [3]: "WRONGB, LMFA00000002, LMFA08040013".
biodb.TRACE[2024-04-15 22:45:23.615][cch$loadFileContent] file.exist = [3]: "TRUE, TRUE, TRUE".
biodb.TRACE[2024-04-15 22:45:23.623][loadFileContents] Loaded 3 files from cache: [3]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv".
biodb.DEBUG[2024-04-15 22:45:23.625][conn$getEntryContent] 3 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 22:45:23.626][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 3 content(s).
biodb.DEBUG[2024-04-15 22:45:23.628][self$createEntryFromContent] Parsing 3 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 22:45:23.629][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:23.631][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:23.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:23.642][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:23.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:23.646][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:23.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:23.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.660][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.662][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:23.677][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:23.679][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:23.681][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:23.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:23.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:23.697][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:23.699][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:23.703][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.705][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.712][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.720][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:23.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:23.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:23.733][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:23.745][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:23.747][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:23.749][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:23.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:23.754][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.763][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:23.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.781][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.789][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.798][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.817][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.823][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.825][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.832][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.840][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.849][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.857][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.876][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.881][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.882][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:23.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:23.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:23.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:23.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:23.891][self$createEntryFromContent] Accession numbers: NA, NA, NA.
biodb.DEBUG[2024-04-15 22:45:23.892][self$createEntryFromContent] Found 3 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-15 22:45:23.893][function(conn, opt)] Entries: [4]: "NULL, NULL, NULL, NULL"
biodb.INFO [2024-04-15 22:45:23.937][biodb::testThat]
biodb.INFO [2024-04-15 22:45:23.939][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-04-15 22:45:23.940][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:23.941][biodb::testThat]
biodb.INFO [2024-04-15 22:45:24.003][biodb::testThat]
biodb.INFO [2024-04-15 22:45:24.004][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-04-15 22:45:24.005][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:24.007][biodb::testThat]
biodb.INFO [2024-04-15 22:45:24.021][biodb::testThat]
biodb.INFO [2024-04-15 22:45:24.023][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-04-15 22:45:24.024][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:24.026][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:24.031][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-04-15 22:45:24.052][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:24.054][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-04-15 22:45:24.056][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:24.331][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.TRACE[2024-04-15 22:45:26.361][ef$get] Asked field names are: name.
biodb.TRACE[2024-04-15 22:45:26.362][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-04-15 22:45:26.364][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:26.365][ef$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:26.366][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:26.367][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-04-15 22:45:26.369][ef$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:26.370][ef$get] fields variable is a list.
biodb.INFO [2024-04-15 22:45:26.372][biodb::testThat]
biodb.INFO [2024-04-15 22:45:26.373][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-04-15 22:45:26.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:26.376][biodb::testThat]
biodb.ERROR[2024-04-15 22:45:26.440][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-04-15 22:45:26.464][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-04-15 22:45:26.480][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 22:45:26.482][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 22:45:26.484][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 22:45:26.485][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 22:45:26.486][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:26.487][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:26.488][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.489][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:26.490][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 22:45:26.508][biodb::testContext]
biodb.INFO [2024-04-15 22:45:26.510][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 22:45:26.512][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-04-15 22:45:26.513][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 22:45:26.515][biodb::testContext]
biodb.INFO [2024-04-15 22:45:26.519][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 22:45:26.523][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 22:45:26.529][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:26.530][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 22:45:26.532][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 22:45:26.533][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.536][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.537][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 22:45:26.539][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 22:45:26.541][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.543][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.547][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 22:45:26.549][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 22:45:26.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.555][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.557][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 22:45:26.559][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 22:45:26.562][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 22:45:26.563][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.567][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.570][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 22:45:26.572][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 22:45:26.574][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 22:45:26.576][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.578][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.580][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.582][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 22:45:26.584][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 22:45:26.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.590][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.592][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 22:45:26.594][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 22:45:26.596][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 22:45:26.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.604][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 22:45:26.607][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 22:45:26.609][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.612][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.648][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 22:45:26.650][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 22:45:26.652][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 22:45:26.654][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.660][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 22:45:26.662][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 22:45:26.664][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 22:45:26.666][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 22:45:26.668][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 22:45:26.670][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 22:45:26.671][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.677][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 22:45:26.679][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 22:45:26.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.684][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.686][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 22:45:26.688][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 22:45:26.690][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.692][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.693][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.695][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 22:45:26.697][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 22:45:26.699][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.701][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.705][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 22:45:26.707][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 22:45:26.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.710][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.713][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 22:45:26.715][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 22:45:26.717][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.723][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 22:45:26.724][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 22:45:26.731][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 22:45:26.733][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.736][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.738][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 22:45:26.740][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 22:45:26.742][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 22:45:26.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.750][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 22:45:26.753][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.755][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 22:45:26.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.759][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:26.761][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.763][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.765][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.767][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.769][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:26.771][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:26.773][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.775][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 22:45:26.777][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:26.779][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.781][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.783][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:26.783][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:26.783][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 22:45:26.783][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 22:45:26.783][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 22:45:26.784][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:26.786][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.788][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.790][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:26.792][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.793][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.795][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.797][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.799][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:26.801][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:26.803][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.805][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.807][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 22:45:26.810][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.812][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 22:45:26.814][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.816][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:26.818][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.821][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.823][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.825][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.827][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 22:45:26.829][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:26.831][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.833][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 22:45:26.835][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:26.837][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.839][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.841][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:26.841][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:26.841][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 22:45:26.841][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 22:45:26.841][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 22:45:26.843][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:26.845][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.846][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.848][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:26.850][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.851][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.853][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.855][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.857][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:26.859][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:26.861][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.863][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.865][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 22:45:26.868][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.870][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 22:45:26.872][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:26.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.880][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.882][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.884][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:26.886][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:26.888][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.889][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 22:45:26.891][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:26.893][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.895][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.897][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.899][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:26.900][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.902][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.904][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:26.906][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.909][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.912][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.914][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:26.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:26.918][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.920][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.922][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 22:45:26.924][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.925][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 22:45:26.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.928][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:26.929][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.931][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.932][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.933][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.935][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 22:45:26.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:26.938][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.939][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 22:45:26.941][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:26.942][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.943][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:26.944][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.946][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:26.947][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.948][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.949][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:26.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:26.951][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:26.952][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:26.954][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.955][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:26.956][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:26.957][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:26.958][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:26.960][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:26.961][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.962][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.966][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:26.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:26.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.975][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.977][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:26.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:26.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.985][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[2024-04-15 22:45:26.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:26.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:26.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:26.997][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:26.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:26.999][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.001][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.008][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.009][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.019][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.029][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.037][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[2024-04-15 22:45:27.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.043][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.051][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.059][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.067][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.069][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.071][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.077][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.087][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.107][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.109][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 22:45:27.113][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 22:45:27.115][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 22:45:27.118][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 22:45:27.121][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 22:45:27.124][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 22:45:27.127][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 22:45:27.130][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 22:45:27.133][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 22:45:27.135][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 22:45:27.137][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 22:45:27.138][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 22:45:27.140][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 22:45:27.142][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 22:45:27.144][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 22:45:27.146][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 22:45:27.148][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 22:45:27.149][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 22:45:27.151][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 22:45:27.153][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 22:45:27.155][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 22:45:27.157][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 22:45:27.159][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 22:45:27.160][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 22:45:27.162][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 22:45:27.164][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 22:45:27.166][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 22:45:27.168][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 22:45:27.170][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 22:45:27.172][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 22:45:27.174][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 22:45:27.176][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 22:45:27.178][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 22:45:27.180][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 22:45:27.182][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 22:45:27.184][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 22:45:27.186][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 22:45:27.188][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 22:45:27.189][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 22:45:27.192][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 22:45:27.193][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 22:45:27.195][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 22:45:27.198][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 22:45:27.201][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 22:45:27.204][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 22:45:27.206][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 22:45:27.208][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 22:45:27.210][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 22:45:27.225][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 22:45:27.228][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 22:45:27.230][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 22:45:27.232][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 22:45:27.234][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 22:45:27.235][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 22:45:27.237][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 22:45:27.239][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 22:45:27.240][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 22:45:27.242][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 22:45:27.243][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 22:45:27.245][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 22:45:27.247][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 22:45:27.248][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 22:45:27.250][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 22:45:27.251][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 22:45:27.253][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 22:45:27.254][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 22:45:27.256][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 22:45:27.258][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 22:45:27.259][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 22:45:27.261][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 22:45:27.262][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 22:45:27.264][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 22:45:27.265][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 22:45:27.267][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 22:45:27.269][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 22:45:27.270][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 22:45:27.272][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 22:45:27.273][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 22:45:27.275][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 22:45:27.276][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 22:45:27.278][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 22:45:27.280][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 22:45:27.281][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 22:45:27.283][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 22:45:27.285][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 22:45:27.286][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:27.287][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.289][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.290][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.291][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[2024-04-15 22:45:27.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.299][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[2024-04-15 22:45:27.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.302][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.303][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.306][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.308][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.309][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.310][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.311][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.318][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.323][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.324][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.327][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.340][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.342][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.345][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.348][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.350][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.358][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[2024-04-15 22:45:27.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.361][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.363][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.371][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.372][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.373][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.374][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.375][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.377][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.379][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.382][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.385][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.389][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.390][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.392][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.393][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.400][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.403][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.404][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.405][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.408][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.413][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[2024-04-15 22:45:27.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.415][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.416][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.417][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.418][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.421][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.422][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:27.423][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:27.424][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:27.425][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:27.426][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:27.427][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:27.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:27.432][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 22:45:27.433][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:27.436][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:27.437][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 22:45:27.438][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:27.439][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:27.441][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:27.442][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:27.443][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:27.444][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:27.445][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:27.447][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:27.448][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:27.449][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 22:45:27.450][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 22:45:27.452][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 22:45:27.453][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:27.454][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:27.454][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:27.455][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:27.457][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:27.458][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:27.459][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:27.460][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:27.461][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:27.462][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:27.464][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 22:45:27.464][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 22:45:27.465][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:27.466][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:27.467][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:27.468][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:27.470][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 22:45:27.471][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 22:45:27.475][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:27.476][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 22:45:27.478][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:27.480][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 22:45:27.481][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 22:45:27.482][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 22:45:27.484][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 22:45:27.485][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 22:45:27.487][biodb::testThat]
biodb.INFO [2024-04-15 22:45:27.489][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-04-15 22:45:27.490][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:27.491][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:27.495][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2024-04-15 22:45:27.509][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:27.511][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cfd52aa1c2e3525a5defd7b7e8bd8bb8".
biodb.TRACE[2024-04-15 22:45:27.513][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:27.533][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content".
biodb.DEBUG[2024-04-15 22:45:27.607][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-04-15 22:45:27.611][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:27.613][cch$loadFileContent] Trying to load 1 files from cache: [1]: "4ae22a112f570b93d2a956448ab71bd0".
biodb.TRACE[2024-04-15 22:45:27.615][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:27.643][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content".
biodb.INFO [2024-04-15 22:45:27.666][biodb::testThat]
biodb.INFO [2024-04-15 22:45:27.668][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-04-15 22:45:27.670][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:27.672][biodb::testThat]
biodb.INFO [2024-04-15 22:45:27.744][biodb::testThat]
biodb.INFO [2024-04-15 22:45:27.745][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-04-15 22:45:27.747][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:27.748][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:27.753][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 22:45:27.759][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:27.760][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-04-15 22:45:27.762][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:27.782][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-04-15 22:45:27.788][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 22:45:27.793][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:27.796][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-04-15 22:45:27.799][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:27.801][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-04-15 22:45:27.809][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-04-15 22:45:27.813][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:27.815][cch$loadFileContent] Trying to load 1 files from cache: [1]: "9edcc233717c530cf0cbf5f73b9c3fc7".
biodb.TRACE[2024-04-15 22:45:27.817][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:27.822][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content".
biodb.DEBUG[2024-04-15 22:45:27.830][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-04-15 22:45:27.833][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:27.835][cch$loadFileContent] Trying to load 1 files from cache: [1]: "be9130a77f849b73da505cd10830451e".
biodb.TRACE[2024-04-15 22:45:27.837][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:27.923][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content".
biodb.DEBUG[2024-04-15 22:45:28.266][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-04-15 22:45:28.272][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:28.275][cch$loadFileContent] Trying to load 1 files from cache: [1]: "6821b039f49696a2484834eb67daa971".
biodb.TRACE[2024-04-15 22:45:28.278][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:28.353][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content".
biodb.INFO [2024-04-15 22:45:28.601][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 22:45:28.603][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 22:45:28.606][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 22:45:28.607][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 22:45:28.609][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:28.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:28.613][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:28.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:28.616][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-04-15 22:45:28.625][biodb::testContext]
biodb.INFO [2024-04-15 22:45:28.627][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 22:45:28.629][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-04-15 22:45:28.631][biodb::testContext] ********************************************************************************
biodb.INFO [2024-04-15 22:45:28.633][biodb::testContext]
biodb.INFO [2024-04-15 22:45:28.638][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-04-15 22:45:28.641][self$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodb/definitions.yml".
biodb.DEBUG[2024-04-15 22:45:28.650][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:28.652][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-04-15 22:45:28.654][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-04-15 22:45:28.656][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.659][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[2024-04-15 22:45:28.661][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-04-15 22:45:28.663][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-04-15 22:45:28.665][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.670][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-04-15 22:45:28.672][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-04-15 22:45:28.674][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.675][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.677][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[2024-04-15 22:45:28.679][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-04-15 22:45:28.681][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-04-15 22:45:28.683][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-04-15 22:45:28.685][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.690][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-04-15 22:45:28.691][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-04-15 22:45:28.693][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-04-15 22:45:28.695][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.698][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[2024-04-15 22:45:28.700][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-04-15 22:45:28.702][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-04-15 22:45:28.704][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.705][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.709][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-04-15 22:45:28.711][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-04-15 22:45:28.713][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-04-15 22:45:28.715][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.716][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.720][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-04-15 22:45:28.722][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-04-15 22:45:28.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.729][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-04-15 22:45:28.731][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-04-15 22:45:28.733][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-04-15 22:45:28.735][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.738][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.740][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-04-15 22:45:28.742][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-04-15 22:45:28.744][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-04-15 22:45:28.746][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-04-15 22:45:28.747][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-04-15 22:45:28.749][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-04-15 22:45:28.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.757][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-04-15 22:45:28.759][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-04-15 22:45:28.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.766][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-04-15 22:45:28.768][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-04-15 22:45:28.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.775][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-04-15 22:45:28.777][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-04-15 22:45:28.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.784][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-04-15 22:45:28.786][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-04-15 22:45:28.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.791][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.793][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-04-15 22:45:28.795][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-04-15 22:45:28.796][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.800][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.802][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-04-15 22:45:28.804][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-04-15 22:45:28.810][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-04-15 22:45:28.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.817][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-04-15 22:45:28.819][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-04-15 22:45:28.821][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-04-15 22:45:28.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:28.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:28.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:28.829][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-04-15 22:45:28.832][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.834][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-04-15 22:45:28.836][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.838][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:28.840][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.842][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.843][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.845][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.847][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:28.849][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:28.851][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.853][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-04-15 22:45:28.855][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:28.857][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.859][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.861][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:28.861][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:28.861][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 22:45:28.861][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 22:45:28.861][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 22:45:28.863][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:28.865][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:28.867][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:28.868][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:28.870][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:28.872][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:28.874][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.876][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:28.880][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:28.881][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.883][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.886][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-04-15 22:45:28.889][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.891][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 22:45:28.893][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.895][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:28.897][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.899][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.901][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.903][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.905][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 22:45:28.907][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:28.909][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.910][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-04-15 22:45:28.912][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:28.914][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.916][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.918][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:28.918][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:28.918][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-04-15 22:45:28.918][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-04-15 22:45:28.918][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-04-15 22:45:28.920][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:28.922][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:28.924][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:28.926][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:28.928][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:28.929][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:28.931][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.933][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.935][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:28.937][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:28.939][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.941][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.943][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-04-15 22:45:28.946][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.947][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-04-15 22:45:28.970][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.972][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:28.974][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.978][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:28.981][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:28.983][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:28.985][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:28.987][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-04-15 22:45:28.989][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:28.990][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.992][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:28.994][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:28.996][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:28.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:28.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:29.001][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:29.003][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:29.004][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:29.006][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.008][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.010][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:29.011][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:29.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:29.015][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.017][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-04-15 22:45:29.020][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.022][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-04-15 22:45:29.023][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.025][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:29.027][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.029][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.031][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:29.032][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.034][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-04-15 22:45:29.036][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:29.038][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:29.040][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-04-15 22:45:29.041][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:29.043][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.045][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.047][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.048][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:29.050][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:29.052][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:29.053][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:29.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:29.057][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:29.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.060][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.062][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:29.064][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:29.065][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:29.067][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.070][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:29.071][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.073][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.075][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.081][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.091][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.102][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.107][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.110][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.114][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.118][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.125][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.161][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.168][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.177][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.195][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.197][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.204][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.208][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.210][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.212][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.214][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.218][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.221][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[2024-04-15 22:45:29.223][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-04-15 22:45:29.226][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-04-15 22:45:29.228][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-04-15 22:45:29.231][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-04-15 22:45:29.234][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-04-15 22:45:29.236][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-04-15 22:45:29.239][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-04-15 22:45:29.241][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-04-15 22:45:29.244][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-04-15 22:45:29.246][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-04-15 22:45:29.249][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-04-15 22:45:29.251][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-04-15 22:45:29.253][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-04-15 22:45:29.256][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-04-15 22:45:29.258][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-04-15 22:45:29.261][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 22:45:29.263][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-04-15 22:45:29.266][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-04-15 22:45:29.268][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-04-15 22:45:29.271][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-04-15 22:45:29.273][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-04-15 22:45:29.275][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-04-15 22:45:29.278][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-04-15 22:45:29.280][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-04-15 22:45:29.283][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-04-15 22:45:29.285][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-04-15 22:45:29.288][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-04-15 22:45:29.291][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-04-15 22:45:29.293][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-04-15 22:45:29.296][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-04-15 22:45:29.298][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-04-15 22:45:29.301][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-04-15 22:45:29.303][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-04-15 22:45:29.306][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-04-15 22:45:29.308][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-04-15 22:45:29.311][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-04-15 22:45:29.314][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-04-15 22:45:29.316][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-04-15 22:45:29.319][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-04-15 22:45:29.321][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-04-15 22:45:29.324][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-04-15 22:45:29.326][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-04-15 22:45:29.329][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-04-15 22:45:29.331][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-04-15 22:45:29.334][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-04-15 22:45:29.336][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-04-15 22:45:29.339][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-04-15 22:45:29.342][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-04-15 22:45:29.344][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-04-15 22:45:29.347][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-04-15 22:45:29.349][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-04-15 22:45:29.352][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-04-15 22:45:29.354][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-04-15 22:45:29.357][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-04-15 22:45:29.359][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-04-15 22:45:29.362][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-04-15 22:45:29.364][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-04-15 22:45:29.367][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-04-15 22:45:29.369][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-04-15 22:45:29.372][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-04-15 22:45:29.374][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-04-15 22:45:29.377][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-04-15 22:45:29.380][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-04-15 22:45:29.382][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-04-15 22:45:29.385][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-04-15 22:45:29.387][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-04-15 22:45:29.390][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-04-15 22:45:29.392][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-04-15 22:45:29.395][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-04-15 22:45:29.397][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-04-15 22:45:29.400][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-04-15 22:45:29.402][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-04-15 22:45:29.405][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-04-15 22:45:29.407][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-04-15 22:45:29.410][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-04-15 22:45:29.412][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-04-15 22:45:29.415][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-04-15 22:45:29.417][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-04-15 22:45:29.420][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-04-15 22:45:29.422][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-04-15 22:45:29.425][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-04-15 22:45:29.427][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-04-15 22:45:29.430][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-04-15 22:45:29.433][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-04-15 22:45:29.436][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-04-15 22:45:29.438][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-04-15 22:45:29.440][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.443][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.447][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.449][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.451][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.454][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.458][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.460][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.472][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.476][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.478][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.479][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.482][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.483][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.485][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.488][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.489][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.491][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.493][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.494][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.496][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.499][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.502][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.508][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.511][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.516][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.519][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.521][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.523][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.542][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.549][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.551][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.553][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.554][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.560][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.562][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.564][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[2024-04-15 22:45:29.566][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.567][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.568][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.570][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.571][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.573][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[2024-04-15 22:45:29.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.576][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.579][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.581][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.585][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.586][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.588][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.589][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.593][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.597][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[2024-04-15 22:45:29.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.600][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.606][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.609][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.611][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.618][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.622][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.627][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.631][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.637][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.640][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.644][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.648][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-04-15 22:45:29.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-04-15 22:45:29.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:29.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:29.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:29.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:29.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:29.659][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[2024-04-15 22:45:29.664][biodb$loadDefinitions] Load definitions from file "F:/biocbuild/bbs-3.18-bioc/R/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-04-15 22:45:29.667][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:29.670][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:29.672][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.675][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.677][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-04-15 22:45:29.679][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.681][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.683][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.685][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.686][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-04-15 22:45:29.688][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-04-15 22:45:29.690][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.692][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-04-15 22:45:29.694][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-04-15 22:45:29.696][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-04-15 22:45:29.698][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-04-15 22:45:29.700][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-04-15 22:45:29.700][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-04-15 22:45:29.702][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-04-15 22:45:29.704][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:29.705][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:29.707][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-04-15 22:45:29.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-04-15 22:45:29.711][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-04-15 22:45:29.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-04-15 22:45:29.715][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-04-15 22:45:29.715][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-04-15 22:45:29.717][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-04-15 22:45:29.719][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-04-15 22:45:29.721][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-04-15 22:45:29.723][self$setPropertyValue]
biodb.DEBUG[2024-04-15 22:45:29.725][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-04-15 22:45:29.728][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-04-15 22:45:29.733][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:29.735][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-04-15 22:45:29.737][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-04-15 22:45:29.741][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-04-15 22:45:29.743][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 22:45:29.745][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-04-15 22:45:29.748][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-04-15 22:45:29.750][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-04-15 22:45:29.753][biodb::testThat]
biodb.INFO [2024-04-15 22:45:29.755][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-04-15 22:45:29.757][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-04-15 22:45:29.758][biodb::testThat]
biodb.DEBUG[2024-04-15 22:45:29.765][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-04-15 22:45:29.773][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-04-15 22:45:29.776][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-04-15 22:45:29.779][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-04-15 22:45:29.963][loadFileContents] Loaded 1 files from cache: [1]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-04-15 22:45:31.818][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-04-15 22:45:31.820][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-04-15 22:45:31.824][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-04-15 22:45:31.826][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-04-15 22:45:31.833][loadFileContents] Loaded 2 files from cache: [2]: "C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, C:\Users\biocbuild\AppData\Local/R/cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-04-15 22:45:31.835][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-04-15 22:45:31.836][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-04-15 22:45:31.838][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-04-15 22:45:31.840][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:31.841][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:31.842][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:31.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:31.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:31.853][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:31.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:31.858][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.863][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:31.873][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:31.874][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:31.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:31.883][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:31.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:31.885][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:31.886][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.TRACE[2024-04-15 22:45:31.888][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.891][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.892][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.893][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-04-15 22:45:31.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.903][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.925][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.930][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.935][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.943][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-04-15 22:45:31.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-04-15 22:45:31.962][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-04-15 22:45:31.963][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-04-15 22:45:31.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-04-15 22:45:31.967][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-04-15 22:45:31.969][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-04-15 22:45:31.973][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-04-15 22:45:31.976][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:31.978][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:31.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:31.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:31.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:31.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:31.996][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:31.999][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-04-15 22:45:32.001][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-04-15 22:45:32.003][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:32.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:32.017][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:32.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:32.021][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:32.023][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-04-15 22:45:32.025][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-04-15 22:45:32.027][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-04-15 22:45:32.029][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-04-15 22:45:32.042][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-04-15 22:45:32.045][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-04-15 22:45:32.047][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-04-15 22:45:32.049][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-04-15 22:45:32.051][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-04-15 22:45:32.053][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-04-15 22:45:32.055][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-04-15 22:45:32.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-04-15 22:45:32.059][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-04-15 22:45:32.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 96 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Error ('test_100_generic.R:16:1'): RT unit is defined when there is an RT value. ──
Error in `eval_bare(expr, quo_get_env(quo))`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(...)
4. └─testthat::quasi_label(enquo(object), label, arg = "object")
5. └─rlang::eval_bare(expr, quo_get_env(quo))
── Failure ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
!is.null(entry) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by searchable field ──
Error in `entry$getFieldValue(f)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can search for an entry by name. ────
!is.null(entry) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for an entry by name. ──────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─opt$refEntries$getRealEntry(id)
4. └─self$getRealEntries(ids = id)
5. └─testthat::expect_false(any(vapply(entries, is.null, FUN.VALUE = TRUE)))
── Failure ('test_100_generic.R:16:1'): We can load an entry from the database. ──
`e` inherits from `'NULL'` not `'character'`.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_is(e, "BiodbEntry")
── Failure ('test_100_generic.R:16:1'): We can search for a compound ───────────
!is.null(entry) is not TRUE
`actual`: FALSE
`expected`: TRUE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_true(!is.null(entry))
── Error ('test_100_generic.R:16:1'): We can search for a compound ─────────────
Error in `entry$getFieldValue("name")`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(db = `<LpdmpsSC>`, opt = `<named list>`)
── Error ('test_100_generic.R:16:1'): annotateMzValues() accepts a single vector. ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
4. └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): ppm tolerance works in annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
4. └─biodb (local) FUN(X[[i]], ...)
── Error ('test_100_generic.R:16:1'): Input data frame is not modified by annotateMzValues() ──
Error in `e$hasField(mf)`: attempt to apply non-function
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─base::vapply(entries, function(e) e$hasField(mf), FUN.VALUE = TRUE)
4. └─biodb (local) FUN(X[[i]], ...)
── Failure ('test_100_generic.R:16:1'): One wrong entry does not block the retrieval of good ones ──
any(vapply(entries[2:length(entries)], is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 14 | WARN 0 | SKIP 0 | PASS 96 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 3.23 | 1.67 | 4.91 | |
| LipidmapsStructureEntry | 0.85 | 0.03 | 0.88 | |