| Back to Multiple platform build/check report for BioC 3.19: simplified long |
|
This page was generated on 2024-07-12 17:42 -0400 (Fri, 12 Jul 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4741 |
| palomino7 | Windows Server 2022 Datacenter | x64 | 4.4.1 (2024-06-14 ucrt) -- "Race for Your Life" | 4483 |
| merida1 | macOS 12.7.4 Monterey | x86_64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4512 |
| kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.4.1 (2024-06-14) -- "Race for Your Life" | 4461 |
| 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 204/2300 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino7 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| merida1 | macOS 12.7.4 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
|
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: 1.10.0 |
| Command: /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz |
| StartedAt: 2024-07-11 12:31:18 -0400 (Thu, 11 Jul 2024) |
| EndedAt: 2024-07-11 12:33:55 -0400 (Thu, 11 Jul 2024) |
| EllapsedTime: 157.0 seconds |
| RetCode: 1 |
| Status: ERROR |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: NA |
##############################################################################
##############################################################################
###
### Running command:
###
### /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings biodbLipidmaps_1.10.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: aarch64-apple-darwin20
* R was compiled by
Apple clang version 14.0.0 (clang-1400.0.29.202)
GNU Fortran (GCC) 12.2.0
* running under: macOS Ventura 13.6.6
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.10.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘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 code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking whether startup messages can be suppressed ... 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 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/Users/biocbuild/bbs-3.19-bioc/meat/biodbLipidmaps.Rcheck/00check.log’
for details.
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/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 Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package can be loaded from final location Warning in fun(libname, pkgname) : Package 'biodbLipidmaps' is deprecated and will be removed from Bioconductor version 3.20 ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
Copyright (C) 2024 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20
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)
Warning message:
In fun(libname, pkgname) :
Package 'biodbLipidmaps' is deprecated and will be removed from
Bioconductor version 3.20
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-07-11 12:32:11.733][biodb::testContext]
biodb.INFO [2024-07-11 12:32:11.739][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-11 12:32:11.740][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-07-11 12:32:11.741][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-11 12:32:11.742][biodb::testContext]
biodb.INFO [2024-07-11 12:32:11.752][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-11 12:32:11.754][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-11 12:32:11.765][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:32:11.766][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-11 12:32:11.767][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-11 12:32:11.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.771][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-11 12:32:11.809][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-11 12:32:11.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.813][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-11 12:32:11.814][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-11 12:32:11.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.818][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-11 12:32:11.819][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-11 12:32:11.820][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-11 12:32:11.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.823][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-11 12:32:11.824][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-11 12:32:11.825][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-11 12:32:11.826][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.828][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-11 12:32:11.829][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-11 12:32:11.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.831][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.832][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-11 12:32:11.833][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-11 12:32:11.834][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-11 12:32:11.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.837][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-11 12:32:11.838][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-11 12:32:11.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.840][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.841][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-11 12:32:11.842][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-11 12:32:11.843][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-11 12:32:11.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.846][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-11 12:32:11.846][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-11 12:32:11.847][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-11 12:32:11.848][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-11 12:32:11.849][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-11 12:32:11.850][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-11 12:32:11.851][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.852][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.853][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-11 12:32:11.854][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-11 12:32:11.854][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.857][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-11 12:32:11.858][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-11 12:32:11.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.860][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.861][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-11 12:32:11.862][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-11 12:32:11.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.863][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.864][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.865][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-11 12:32:11.866][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-11 12:32:11.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.869][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-11 12:32:11.870][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-11 12:32:11.871][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.873][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-11 12:32:11.874][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-11 12:32:11.888][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-11 12:32:11.889][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.890][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.893][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-11 12:32:11.894][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-11 12:32:11.895][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-11 12:32:11.896][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:11.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:11.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:11.902][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-11 12:32:11.941][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:11.958][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-11 12:32:11.959][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:11.960][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:32:11.961][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:11.962][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:32:11.963][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:11.964][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:32:11.965][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:32:11.965][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:32:11.966][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:11.967][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-11 12:32:11.968][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:32:11.969][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:11.970][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:11.970][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:32:11.970][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:32:11.970][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-11 12:32:11.970][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-11 12:32:11.970][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-11 12:32:11.971][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:32:11.972][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:11.973][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:11.974][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:32:11.975][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:11.975][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:11.976][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:32:11.977][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:11.978][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:32:11.979][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:32:11.979][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:11.980][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:11.981][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-11 12:32:11.983][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:11.984][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-11 12:32:11.985][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:11.986][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:32:11.987][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:11.995][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:32:11.996][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:11.997][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:32:11.998][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-11 12:32:11.999][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:32:12.000][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.000][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-11 12:32:12.001][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:32:12.002][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.003][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.004][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:32:12.004][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:32:12.004][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-11 12:32:12.004][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-11 12:32:12.004][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-11 12:32:12.005][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:32:12.006][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.006][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.007][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:32:12.008][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.009][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.010][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.010][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.011][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:32:12.012][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:32:12.013][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.014][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.015][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-11 12:32:12.016][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.017][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-11 12:32:12.018][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.019][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:32:12.020][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.021][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.022][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.023][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.024][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:32:12.025][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:32:12.025][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.026][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-11 12:32:12.027][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:32:12.028][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.029][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.030][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.030][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:32:12.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.033][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:32:12.034][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.035][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.036][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.037][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:32:12.037][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:32:12.038][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.039][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.040][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-11 12:32:12.042][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.043][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-11 12:32:12.043][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.044][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:32:12.045][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.046][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.047][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.047][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.048][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-11 12:32:12.049][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:32:12.050][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.051][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-11 12:32:12.051][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:32:12.052][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.053][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.054][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.055][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:32:12.055][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.056][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.057][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:32:12.058][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.058][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.059][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.060][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.061][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:32:12.062][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:32:12.062][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.063][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.068][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:32:12.069][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.071][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.072][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.076][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.077][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.078][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.081][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.083][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.086][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.087][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.088][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.089][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[2024-07-11 12:32:12.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.094][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.097][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[2024-07-11 12:32:12.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.098][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.099][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.104][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.105][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.108][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.112][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.113][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.116][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.121][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.123][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.128][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.129][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.134][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.135][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.136][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-11 12:32:12.142][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-11 12:32:12.144][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-11 12:32:12.145][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-11 12:32:12.146][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-11 12:32:12.148][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-11 12:32:12.149][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-11 12:32:12.151][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-11 12:32:12.152][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-11 12:32:12.153][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-11 12:32:12.155][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-11 12:32:12.156][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-11 12:32:12.163][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-11 12:32:12.164][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-11 12:32:12.166][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-11 12:32:12.167][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-11 12:32:12.168][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-11 12:32:12.169][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-11 12:32:12.170][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-11 12:32:12.171][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-11 12:32:12.172][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-11 12:32:12.173][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-11 12:32:12.175][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-11 12:32:12.176][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-11 12:32:12.177][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-11 12:32:12.178][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-11 12:32:12.179][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-11 12:32:12.180][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-11 12:32:12.181][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-11 12:32:12.182][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-11 12:32:12.184][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-11 12:32:12.185][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-11 12:32:12.186][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-11 12:32:12.187][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-11 12:32:12.188][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-11 12:32:12.189][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-11 12:32:12.190][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-11 12:32:12.191][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-11 12:32:12.193][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-11 12:32:12.194][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-11 12:32:12.195][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-11 12:32:12.196][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-11 12:32:12.197][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-11 12:32:12.198][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-11 12:32:12.199][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-11 12:32:12.201][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-11 12:32:12.202][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-11 12:32:12.203][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-11 12:32:12.204][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-11 12:32:12.205][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-11 12:32:12.206][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-11 12:32:12.207][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-11 12:32:12.208][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-11 12:32:12.209][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-11 12:32:12.211][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-11 12:32:12.212][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-11 12:32:12.214][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-11 12:32:12.215][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-11 12:32:12.217][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-11 12:32:12.218][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-11 12:32:12.219][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-11 12:32:12.221][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-11 12:32:12.222][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-11 12:32:12.223][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-11 12:32:12.225][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-11 12:32:12.226][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-11 12:32:12.227][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-11 12:32:12.228][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-11 12:32:12.230][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-11 12:32:12.231][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-11 12:32:12.232][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-11 12:32:12.233][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-11 12:32:12.234][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-11 12:32:12.235][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-11 12:32:12.237][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-11 12:32:12.238][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-11 12:32:12.239][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-11 12:32:12.240][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-11 12:32:12.241][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-11 12:32:12.242][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-11 12:32:12.243][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-11 12:32:12.245][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-11 12:32:12.246][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-11 12:32:12.252][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-11 12:32:12.254][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-11 12:32:12.258][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:32:12.260][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.260][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.261][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.263][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.273][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.274][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.278][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.279][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.280][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.285][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.287][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.288][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.289][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.291][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.292][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.296][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.298][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.298][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.299][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[2024-07-11 12:32:12.300][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.305][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.324][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.326][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.328][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.329][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.331][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[2024-07-11 12:32:12.332][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.334][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.337][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[2024-07-11 12:32:12.338][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.340][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.342][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[2024-07-11 12:32:12.343][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.344][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.352][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.358][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[2024-07-11 12:32:12.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.360][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.362][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.363][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:32:12.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.367][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:12.371][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-11 12:32:12.381][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:32:12.383][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.384][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.385][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.386][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:32:12.387][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.387][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.388][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.389][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.390][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:32:12.391][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:32:12.392][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.393][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-11 12:32:12.393][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-11 12:32:12.394][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-11 12:32:12.395][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-11 12:32:12.396][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:32:12.396][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:32:12.397][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:32:12.398][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.399][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.399][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:32:12.400][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:32:12.401][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:32:12.402][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:32:12.403][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-11 12:32:12.403][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-11 12:32:12.404][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:32:12.405][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:32:12.406][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-11 12:32:12.407][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:32:12.413][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-11 12:32:12.414][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-11 12:32:12.447][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:32:12.449][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-11 12:32:12.454][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:32:12.460][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-11 12:32:12.466][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-11 12:32:12.467][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-11 12:32:12.468][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-11 12:32:12.469][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-11 12:32:12.483][biodb::testThat]
biodb.INFO [2024-07-11 12:32:12.484][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-07-11 12:32:12.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:12.486][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:12.492][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-07-11 12:32:12.495][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-11 12:32:12.500][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-11 12:32:12.512][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:12.513][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:12.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:12.532][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:12.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:12.534][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:12.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:12.551][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.584][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.585][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.587][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:32:12.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:32:12.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.590][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:12.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:12.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.594][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:12.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:12.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.598][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:12.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:12.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.627][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:12.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:12.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.630][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.632][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:12.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:12.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.635][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:12.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:12.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.639][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:12.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:12.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.641][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.642][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:12.643][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:12.644][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.646][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:12.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:12.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.649][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:12.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:12.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.652][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.656][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.660][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:12.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.663][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-11 12:32:12.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.670][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.674][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:12.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.747][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.752][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.796][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.796][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.797][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.802][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.805][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.809][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.818][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.819][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.822][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.823][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.825][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.829][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:12.832][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-11 12:32:12.835][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:32:12.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:32:12.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.839][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:32:12.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:32:12.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.843][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-11 12:32:12.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-11 12:32:12.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.846][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-11 12:32:12.847][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-11 12:32:12.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.871][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.896][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.910][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.911][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.914][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.920][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.927][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.928][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.929][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.931][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.932][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.935][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.939][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:12.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.953][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.957][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.964][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.965][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.966][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.966][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.967][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:12.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:12.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.982][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.984][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.985][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.986][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.987][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.988][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.989][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.990][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.991][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.993][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.993][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:12.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:12.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:12.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:12.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.007][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.014][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.018][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.019][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.019][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.020][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.021][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.033][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.037][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.040][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.052][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.052][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.054][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.055][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.056][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.057][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.067][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.071][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.074][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.075][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.076][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.077][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.078][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.079][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.079][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.080][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.081][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.100][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.103][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.107][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.107][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.110][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.122][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.123][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.124][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.125][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.130][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.131][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.132][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.133][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.138][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.140][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.140][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.141][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.146][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.147][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.148][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.149][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.154][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.155][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.156][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.157][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.162][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.163][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.164][ef$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:13.173][biodb::testThat]
biodb.INFO [2024-07-11 12:32:13.174][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-07-11 12:32:13.175][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:13.176][biodb::testThat]
biodb.DEBUG[2024-07-11 12:32:13.191][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-07-11 12:32:13.209][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-11 12:32:13.214][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-07-11 12:32:13.216][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:32:13.217][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-07-11 12:32:13.218][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-11 12:32:13.242][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-11 12:32:13.243][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-11 12:32:13.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:13.246][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:13.247][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:13.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:13.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:13.254][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:13.255][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:13.259][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.260][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:32:13.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:32:13.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.270][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:32:13.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:32:13.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.274][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:13.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:13.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.277][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:13.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:13.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.284][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:13.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.287][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.290][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.291][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.291][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:13.292][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.294][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:13.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.297][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:13.298][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:13.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.301][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.304][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:13.305][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:13.306][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.307][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.311][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.314][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:13.315][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.316][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.317][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.318][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-11 12:32:13.318][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.321][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.327][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:13.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.331][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.339][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.340][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.341][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.344][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.348][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.351][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.354][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:13.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:13.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.357][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.357][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:13.358][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:13.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.361][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.364][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:13.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:13.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.366][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.367][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.369][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.374][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:13.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:13.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:13.387][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-07-11 12:32:13.388][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-07-11 12:32:13.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-07-11 12:32:13.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.392][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-07-11 12:32:13.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-07-11 12:32:13.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-07-11 12:32:13.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-07-11 12:32:13.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:13.407][biodb::testThat]
biodb.INFO [2024-07-11 12:32:13.408][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-07-11 12:32:13.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:13.409][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:13.412][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.413][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.414][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.415][ef$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:13.416][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-07-11 12:32:13.441][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.442][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.444][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.445][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.447][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:13.448][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:13.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:13.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:13.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:13.454][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-11 12:32:13.460][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-11 12:32:13.488][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:13.489][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:32:13.490][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2024-07-11 12:32:13.902][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2024-07-11 12:32:14.221][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:14.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2024-07-11 12:32:14.240][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2024-07-11 12:32:14.243][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-07-11 12:32:14.257][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:14.259][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:14.260][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.261][ef$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:14.265][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.266][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-07-11 12:32:14.267][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:14.268][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:14.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:14.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:14.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.300][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:14.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:14.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.303][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:14.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:14.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:14.422][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-11 12:32:14.426][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-11 12:32:14.448][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-11 12:32:14.450][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:32:14.451][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-07-11 12:32:14.469][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.470][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-07-11 12:32:14.471][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:14.472][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:14.495][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.499][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.500][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.503][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-11 12:32:14.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-11 12:32:14.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.507][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-11 12:32:14.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-11 12:32:14.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.560][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.565][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:32:14.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.568][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-11 12:32:14.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-11 12:32:14.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.572][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-11 12:32:14.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-11 12:32:14.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:14.584][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.585][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-07-11 12:32:14.586][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:14.587][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.596][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.597][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-07-11 12:32:14.599][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:14.600][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.608][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.609][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-07-11 12:32:14.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:14.611][biodb::testThat]
biodb.DEBUG[2024-07-11 12:32:14.615][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-07-11 12:32:14.889][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-07-11 12:32:14.984][biodb::testThat]
biodb.INFO [2024-07-11 12:32:14.985][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-07-11 12:32:14.986][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:14.987][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:14.992][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:14.993][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:14.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.995][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:14.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:14.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:14.998][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:14.998][ef$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:15.000][biodb::testThat]
biodb.INFO [2024-07-11 12:32:15.001][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-07-11 12:32:15.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:15.003][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:15.012][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:15.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:15.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.025][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:15.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:15.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.028][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:15.029][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:15.030][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:15.109][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-11 12:32:15.113][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-11 12:32:15.114][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-11 12:32:15.115][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:32:15.117][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-07-11 12:32:15.184][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-07-11 12:32:15.188][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-11 12:32:15.190][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-07-11 12:32:15.191][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:32:15.192][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-07-11 12:32:15.207][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-11 12:32:15.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-11 12:32:15.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.216][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:15.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:15.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.225][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.227][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.228][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.229][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.230][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.231][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.239][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.242][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:15.245][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:15.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:15.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:15.258][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-07-11 12:32:15.275][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:15.276][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:32:15.293][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-07-11 12:32:19.184][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-07-11 12:32:24.445][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:24.448][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2024-07-11 12:32:24.460][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2024-07-11 12:32:25.898][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2024-07-11 12:32:25.902][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:25.903][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:32:25.906][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2024-07-11 12:32:26.220][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2024-07-11 12:32:26.542][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:26.544][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2024-07-11 12:32:26.549][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2024-07-11 12:32:26.573][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2024-07-11 12:32:26.577][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:26.579][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:26.580][rule$waitAsNeeded] Wait 0.324528 second(s).
biodb.TRACE[2024-07-11 12:32:27.057][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2024-07-11 12:32:27.312][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2024-07-11 12:32:27.618][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:27.621][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2024-07-11 12:32:27.626][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2024-07-11 12:32:27.645][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:27.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:27.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:27.658][biodb::testThat]
biodb.INFO [2024-07-11 12:32:27.659][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-07-11 12:32:27.660][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:27.661][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:27.665][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-11 12:32:27.666][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-11 12:32:27.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:27.668][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:27.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:27.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:27.672][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:27.676][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:27.679][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:27.683][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:27.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:27.686][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:27.691][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:27.692][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:27.693][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:27.699][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:27.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:27.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:27.702][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:27.706][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-07-11 12:32:27.711][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:27.712][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:27.713][rule$waitAsNeeded] Wait 0.342664 second(s).
biodb.TRACE[2024-07-11 12:32:28.208][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2024-07-11 12:32:31.823][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2024-07-11 12:32:36.046][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:36.056][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-07-11 12:32:36.065][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-07-11 12:32:37.627][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-07-11 12:32:37.671][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-11 12:32:37.673][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2024-07-11 12:32:37.674][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-11 12:32:37.675][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-11 12:32:37.676][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-11 12:32:37.677][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-11 12:32:37.678][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-11 12:32:37.679][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-11 12:32:37.693][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:37.694][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:37.695][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:37.700][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:37.701][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:37.702][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:37.703][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:37.704][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-07-11 12:32:37.707][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:37.708][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:32:37.709][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-07-11 12:32:38.028][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-07-11 12:32:38.330][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:38.333][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-07-11 12:32:38.336][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-07-11 12:32:38.339][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:38.340][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:38.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:38.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:38.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:38.347][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:38.348][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[2024-07-11 12:32:38.349][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-07-11 12:32:38.352][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:38.353][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:38.354][rule$waitAsNeeded] Wait 0.355775 second(s).
biodb.TRACE[2024-07-11 12:32:38.761][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-07-11 12:32:39.085][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-07-11 12:32:39.395][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:39.398][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-07-11 12:32:39.402][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-07-11 12:32:39.404][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2024-07-11 12:32:39.406][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-11 12:32:39.407][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-11 12:32:39.409][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-11 12:32:39.410][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:39.411][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:39.412][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:39.419][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:39.420][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:39.421][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:39.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:39.427][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.436][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:32:39.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:32:39.437][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.438][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.439][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:32:39.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:32:39.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.443][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:39.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:39.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.447][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:39.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:39.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.451][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.455][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.459][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.463][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.467][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:39.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.471][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:39.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.475][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:39.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:39.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.479][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:39.480][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:39.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.483][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.487][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.492][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:39.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.496][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-11 12:32:39.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.499][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.502][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.503][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.507][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:39.508][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.509][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.511][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.513][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.514][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.515][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.519][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.520][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.521][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.523][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.527][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.530][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.531][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.536][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:39.541][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:39.542][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:39.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:39.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:39.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:39.551][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:39.552][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:39.557][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.558][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.559][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.560][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.562][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.567][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:32:39.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:32:39.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.572][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:39.573][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:32:39.574][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.575][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.576][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:39.577][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:32:39.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.580][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.582][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.583][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.584][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:32:39.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.608][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.610][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.613][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.613][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:32:39.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.616][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:39.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.618][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.619][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:32:39.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.622][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:39.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:39.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.626][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:32:39.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:32:39.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.630][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.638][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:39.639][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.640][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.641][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-11 12:32:39.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.645][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.648][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:32:39.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.652][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:32:39.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:32:39.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.657][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.658][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.659][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.660][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.664][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.666][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.667][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.668][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.669][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.673][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.679][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.680][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.681][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.682][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.683][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.688][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.689][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.693][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.694][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.695][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.696][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:32:39.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:32:39.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:39.700][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-07-11 12:32:39.710][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-11 12:32:39.712][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:39.713][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:39.713][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:39.719][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:39.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:39.721][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:39.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:39.723][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.727][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.730][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.731][private$selectFields]
biodb.TRACE[2024-07-11 12:32:39.732][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:39.733][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:39.734][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.735][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.736][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.736][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.737][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.738][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.740][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.740][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.741][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.742][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.743][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.744][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.745][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.746][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.747][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.747][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:39.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.752][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.753][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.756][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.770][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-11 12:32:39.771][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:39.772][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:39.773][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:39.779][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:39.780][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:39.781][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:39.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:39.783][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.786][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.790][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.790][private$selectFields]
biodb.TRACE[2024-07-11 12:32:39.791][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:39.792][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:39.793][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.793][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.794][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.795][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.796][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.796][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.797][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.798][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.799][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.800][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.800][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.801][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.802][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.803][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.803][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.804][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:39.805][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.808][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.811][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.815][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.816][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-11 12:32:39.817][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:39.818][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:39.819][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:39.824][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:39.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:39.826][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:39.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.835][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.835][private$selectFields]
biodb.TRACE[2024-07-11 12:32:39.836][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:39.837][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:39.838][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.838][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.839][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.840][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.841][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.842][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.843][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.843][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.844][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.845][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.846][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:39.847][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.848][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.849][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.850][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.850][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:39.851][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.855][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.859][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:39.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.862][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-11 12:32:39.863][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-11 12:32:39.864][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-11 12:32:39.876][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:39.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:39.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:39.884][biodb::testThat]
biodb.INFO [2024-07-11 12:32:39.885][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-07-11 12:32:39.886][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:39.886][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:39.890][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-11 12:32:39.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-11 12:32:39.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.894][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:39.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:39.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.913][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.916][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:39.924][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:39.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:39.926][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:39.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:39.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:39.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:39.987][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:39.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:39.989][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:39.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:39.993][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2024-07-11 12:32:39.997][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:39.998][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:32:40.000][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-07-11 12:32:43.613][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-07-11 12:32:48.548][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:32:48.554][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-07-11 12:32:48.565][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-07-11 12:32:50.113][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-11 12:32:50.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:50.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:50.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:50.144][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:50.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:50.146][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:50.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:50.159][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.163][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.164][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.165][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.185][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.187][private$selectFields]
biodb.TRACE[2024-07-11 12:32:50.188][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:50.189][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:50.190][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.191][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.192][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.192][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.193][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.194][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.196][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.196][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.197][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.198][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.211][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.213][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.214][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.215][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.215][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.216][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:50.217][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.219][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.221][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.225][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.230][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-11 12:32:50.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:50.232][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:50.233][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:50.238][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:50.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:50.240][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:50.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:50.243][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.247][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.252][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.253][private$selectFields]
biodb.TRACE[2024-07-11 12:32:50.254][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:50.255][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:50.256][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.257][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.258][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.260][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.261][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.262][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.262][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.263][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.264][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.265][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.266][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.270][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.272][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.273][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.274][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:50.275][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.294][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.298][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.302][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-11 12:32:50.304][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:50.305][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:50.305][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:50.312][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:50.313][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:50.314][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:50.314][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.TRACE[2024-07-11 12:32:50.316][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.323][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.324][private$selectFields]
biodb.TRACE[2024-07-11 12:32:50.325][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:50.326][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:50.327][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.328][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.329][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.331][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.331][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.332][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.334][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.335][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.336][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:50.337][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.338][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.340][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.341][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:50.342][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.343][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.345][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.349][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:50.351][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.352][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.354][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-11 12:32:50.355][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-11 12:32:50.356][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-11 12:32:50.366][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:50.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:50.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:50.375][biodb::testThat]
biodb.INFO [2024-07-11 12:32:50.376][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-07-11 12:32:50.377][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:50.378][biodb::testThat]
biodb.TRACE[2024-07-11 12:32:50.381][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-07-11 12:32:50.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-07-11 12:32:50.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.385][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:50.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-07-11 12:32:50.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.389][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.393][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.394][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.395][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.396][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:50.678][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:32:50.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:50.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:32:50.687][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:50.688][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:50.688][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:50.693][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:50.694][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:50.695][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:50.696][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[2024-07-11 12:32:50.699][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-07-11 12:32:50.703][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-11 12:32:50.704][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-07-11 12:32:50.705][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:32:50.768][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-07-11 12:32:52.027][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-11 12:32:52.029][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:52.030][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:52.031][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:52.037][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:52.038][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:52.038][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:52.039][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:52.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.044][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.046][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.047][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.048][private$selectFields]
biodb.TRACE[2024-07-11 12:32:52.049][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:52.049][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:52.050][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.051][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.052][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.053][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.053][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.054][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.055][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.057][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.058][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.058][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.059][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.060][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.061][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.063][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.063][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:52.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.068][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.071][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.075][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-07-11 12:32:52.076][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:52.077][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:52.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:52.083][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:52.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:52.085][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:52.086][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:52.087][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.090][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.094][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.094][private$selectFields]
biodb.TRACE[2024-07-11 12:32:52.095][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:52.096][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:52.097][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.097][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.098][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.099][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.100][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.101][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.103][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.104][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.105][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.106][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.107][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.108][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.109][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.109][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:52.110][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.114][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.117][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.122][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-07-11 12:32:52.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:52.123][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:52.124][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:52.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:52.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:52.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:52.132][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:32:52.134][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.135][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.137][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.140][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.141][private$selectFields]
biodb.TRACE[2024-07-11 12:32:52.142][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-07-11 12:32:52.143][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:32:52.143][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.144][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.145][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.146][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.147][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.148][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.148][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.149][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.150][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.151][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.152][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:32:52.153][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.153][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.154][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.155][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.156][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-07-11 12:32:52.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.157][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.158][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.159][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.160][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.164][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:32:52.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.166][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:32:52.168][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-07-11 12:32:52.168][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-07-11 12:32:52.169][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-07-11 12:32:52.190][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:52.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-07-11 12:32:52.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:32:52.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-07-11 12:32:52.198][biodb::testThat]
biodb.INFO [2024-07-11 12:32:52.199][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-07-11 12:32:52.200][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:32:52.201][biodb::testThat]
biodb.DEBUG[2024-07-11 12:32:52.203][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-07-11 12:32:52.204][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-07-11 12:32:52.205][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-07-11 12:32:52.207][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-07-11 12:32:52.208][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-11 12:32:52.209][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-11 12:32:52.210][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-11 12:32:52.211][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-11 12:32:52.212][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-11 12:32:52.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:32:52.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:32:52.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:32:52.234][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:32:52.235][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:32:52.236][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:32:52.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:32:52.238][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-07-11 12:32:52.241][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:52.242][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:32:52.243][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:52.511][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:52.512][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:52.513][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:52.515][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:52.788][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:52.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:52.790][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:52.791][rule$waitAsNeeded] Wait 0.452784 second(s).
biodb.TRACE[2024-07-11 12:32:53.395][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:53.691][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:53.692][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:53.693][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:53.694][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:53.978][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:53.980][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:53.981][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:53.982][rule$waitAsNeeded] Wait 0.412895 second(s).
biodb.TRACE[2024-07-11 12:32:54.546][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:54.848][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:54.849][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:54.850][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:54.851][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:55.147][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:55.148][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:55.149][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:55.150][rule$waitAsNeeded] Wait 0.395353 second(s).
biodb.TRACE[2024-07-11 12:32:55.616][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:55.900][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:55.901][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:55.902][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:55.903][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:56.192][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:56.193][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:56.194][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:56.195][rule$waitAsNeeded] Wait 0.420481 second(s).
biodb.TRACE[2024-07-11 12:32:56.767][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:57.069][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:57.071][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:57.072][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:57.073][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:57.331][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:57.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:57.334][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:57.335][rule$waitAsNeeded] Wait 0.432113 second(s).
biodb.TRACE[2024-07-11 12:32:57.918][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:58.202][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:58.203][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:58.204][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:58.205][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:58.485][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:58.486][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:58.487][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:58.488][rule$waitAsNeeded] Wait 0.429868 second(s).
biodb.TRACE[2024-07-11 12:32:59.069][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:32:59.333][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:32:59.334][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:32:59.335][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:32:59.336][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:32:59.553][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:32:59.554][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:32:59.555][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:32:59.556][rule$waitAsNeeded] Wait 0.512577 second(s).
biodb.TRACE[2024-07-11 12:33:00.220][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:33:00.510][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:00.511][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:00.512][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:00.513][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:33:00.695][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:00.696][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:00.697][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:00.698][rule$waitAsNeeded] Wait 0.522174 second(s).
biodb.TRACE[2024-07-11 12:33:01.329][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:33:01.548][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:01.550][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:01.551][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:01.573][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:33:01.838][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:01.839][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:01.840][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:01.841][rule$waitAsNeeded] Wait 0.487148 second(s).
biodb.TRACE[2024-07-11 12:33:02.480][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-07-11 12:33:02.722][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:02.723][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:02.724][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:02.725][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-07-11 12:33:02.970][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-11 12:33:02.973][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-07-11 12:33:02.975][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-11 12:33:02.976][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-07-11 12:33:02.977][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-11 12:33:02.978][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:02.979][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:02.980][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:02.985][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:02.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:02.987][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:02.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:02.989][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:02.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:02.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:02.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:02.992][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:02.993][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:02.994][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:02.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:02.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:02.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:02.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:02.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:02.999][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:02.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:03.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:03.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:03.002][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:03.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:03.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:03.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:03.005][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:03.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:03.006][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:03.007][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:03.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:03.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:03.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:03.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:03.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:03.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:03.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:03.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:33:03.014][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-07-11 12:33:03.015][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-07-11 12:33:03.023][biodb::testThat]
biodb.INFO [2024-07-11 12:33:03.024][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-07-11 12:33:03.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:03.026][biodb::testThat]
biodb.DEBUG[2024-07-11 12:33:03.035][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-07-11 12:33:03.036][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-07-11 12:33:03.037][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-11 12:33:03.039][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-07-11 12:33:03.040][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-07-11 12:33:03.041][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-07-11 12:33:03.042][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-11 12:33:03.043][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-11 12:33:03.044][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-07-11 12:33:03.045][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-07-11 12:33:03.049][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:03.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:03.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:03.056][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:03.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:03.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:03.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:03.059][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-07-11 12:33:03.062][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:03.063][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:03.064][rule$waitAsNeeded] Wait 0.415325 second(s).
biodb.TRACE[2024-07-11 12:33:03.631][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:03.867][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:03.868][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:03.869][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:03.870][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:04.079][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:04.080][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:04.081][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:04.082][rule$waitAsNeeded] Wait 0.54828 second(s).
biodb.TRACE[2024-07-11 12:33:04.782][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:05.026][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:05.028][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:05.029][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:05.030][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:05.249][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:05.250][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:05.251][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:05.252][rule$waitAsNeeded] Wait 0.530152 second(s).
biodb.TRACE[2024-07-11 12:33:05.895][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:06.140][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:06.141][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:06.142][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:06.143][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:06.378][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:06.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:06.380][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:06.381][rule$waitAsNeeded] Wait 0.512943 second(s).
biodb.TRACE[2024-07-11 12:33:06.915][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:07.164][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:07.166][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:07.167][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:07.168][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:07.410][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:07.411][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:07.412][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:07.413][rule$waitAsNeeded] Wait 0.501791 second(s).
biodb.TRACE[2024-07-11 12:33:07.924][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:08.164][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:08.164][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:08.165][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:08.166][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:08.661][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:08.663][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:08.663][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:08.665][rule$waitAsNeeded] Wait 0.258996 second(s).
biodb.TRACE[2024-07-11 12:33:09.032][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:09.284][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:09.285][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:09.286][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:09.287][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:09.521][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:09.522][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:09.523][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:09.524][rule$waitAsNeeded] Wait 0.508274 second(s).
biodb.TRACE[2024-07-11 12:33:10.053][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:10.257][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:10.258][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:10.259][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:10.260][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:10.501][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:10.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:10.503][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:10.504][rule$waitAsNeeded] Wait 0.547702 second(s).
biodb.TRACE[2024-07-11 12:33:11.067][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:11.316][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:11.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:11.318][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:11.319][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:11.771][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:11.772][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:11.773][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:11.774][rule$waitAsNeeded] Wait 0.292532 second(s).
biodb.TRACE[2024-07-11 12:33:12.219][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:12.456][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:12.457][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:12.458][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:12.459][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:12.954][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:12.955][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:12.956][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:12.957][rule$waitAsNeeded] Wait 0.2608 second(s).
biodb.TRACE[2024-07-11 12:33:13.304][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-07-11 12:33:13.555][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:13.556][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:13.557][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:13.557][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-07-11 12:33:13.908][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:13.909][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:13.909][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:13.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:13.913][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:13.913][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:13.914][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:13.914][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:13.915][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-07-11 12:33:13.916][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:13.917][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:13.917][rule$waitAsNeeded] Wait 0.386452 second(s).
biodb.TRACE[2024-07-11 12:33:14.307][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:14.496][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:14.497][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:14.498][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:14.499][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:14.740][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:14.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:14.742][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:14.743][rule$waitAsNeeded] Wait 0.563486 second(s).
biodb.TRACE[2024-07-11 12:33:15.338][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:15.586][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:15.587][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:15.588][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:15.589][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:15.949][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:15.950][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:15.951][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:15.952][rule$waitAsNeeded] Wait 0.385199 second(s).
biodb.TRACE[2024-07-11 12:33:16.489][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:16.742][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:16.743][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:16.744][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:16.745][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:17.000][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:17.001][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:17.002][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:17.003][rule$waitAsNeeded] Wait 0.484926 second(s).
biodb.TRACE[2024-07-11 12:33:17.640][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:17.881][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:17.882][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:17.883][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:17.884][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:18.378][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:18.379][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:18.380][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:18.381][rule$waitAsNeeded] Wait 0.257999 second(s).
biodb.TRACE[2024-07-11 12:33:18.681][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:18.918][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:18.920][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:18.921][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:18.922][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:19.131][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:19.132][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:19.133][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:19.134][rule$waitAsNeeded] Wait 0.546981 second(s).
biodb.TRACE[2024-07-11 12:33:19.832][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:20.070][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:20.071][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:20.073][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:20.074][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:20.302][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:20.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:20.304][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:20.305][rule$waitAsNeeded] Wait 0.526721 second(s).
biodb.TRACE[2024-07-11 12:33:20.971][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:21.207][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:21.208][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:21.210][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:21.211][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:21.450][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:21.451][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:21.452][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:21.453][rule$waitAsNeeded] Wait 0.517441 second(s).
biodb.TRACE[2024-07-11 12:33:22.075][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:22.316][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:22.317][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:22.318][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:22.319][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:22.834][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:22.835][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:22.836][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:22.837][rule$waitAsNeeded] Wait 0.237475 second(s).
biodb.TRACE[2024-07-11 12:33:23.092][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:23.335][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:23.337][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:23.338][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:23.339][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:23.832][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-07-11 12:33:23.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:23.835][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:23.877][rule$waitAsNeeded] Wait 0.256193 second(s).
biodb.TRACE[2024-07-11 12:33:24.286][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-07-11 12:33:24.524][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-07-11 12:33:24.525][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-07-11 12:33:24.526][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-07-11 12:33:24.527][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-07-11 12:33:24.763][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-07-11 12:33:24.765][private$doSaveContentToFile] Saving to cache [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2024-07-11 12:33:24.766][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-07-11 12:33:24.767][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-11 12:33:24.767][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-11 12:33:24.768][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:24.768][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:24.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:24.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:24.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:24.772][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:24.772][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:24.773][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.774][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.776][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:33:24.777][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:24.778][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:24.778][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:24.781][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:24.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:24.782][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:24.782][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:24.783][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.784][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:24.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.785][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.787][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.788][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.790][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.793][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.796][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.799][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.802][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.803][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.806][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.809][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.812][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.814][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:24.815][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:24.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:24.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:24.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:33:24.818][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-07-11 12:33:24.819][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-07-11 12:33:24.820][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-07-11 12:33:24.965][biodb::testThat]
biodb.INFO [2024-07-11 12:33:24.966][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-07-11 12:33:24.966][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:24.966][biodb::testThat]
biodb.INFO [2024-07-11 12:33:24.994][biodb::testThat]
biodb.INFO [2024-07-11 12:33:24.995][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-07-11 12:33:24.995][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:24.996][biodb::testThat]
biodb.INFO [2024-07-11 12:33:25.001][biodb::testThat]
biodb.INFO [2024-07-11 12:33:25.002][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-07-11 12:33:25.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:25.002][biodb::testThat]
biodb.DEBUG[2024-07-11 12:33:25.004][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[2024-07-11 12:33:25.006][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:25.006][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:25.007][rule$waitAsNeeded] Wait 0.27789 second(s).
biodb.TRACE[2024-07-11 12:33:25.287][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-07-11 12:33:29.025][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-07-11 12:33:33.684][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:33.687][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-07-11 12:33:33.699][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-07-11 12:33:34.992][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:34.993][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:34.994][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:34.995][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:34.996][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:34.997][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:34.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:34.998][ef$get] fields variable is a list.
biodb.INFO [2024-07-11 12:33:35.000][biodb::testThat]
biodb.INFO [2024-07-11 12:33:35.001][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-07-11 12:33:35.002][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:35.003][biodb::testThat]
biodb.ERROR[2024-07-11 12:33:35.019][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-07-11 12:33:35.038][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-07-11 12:33:35.053][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-11 12:33:35.055][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-11 12:33:35.056][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-11 12:33:35.057][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-11 12:33:35.058][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.058][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.059][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.061][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.061][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-11 12:33:35.073][biodb::testContext]
biodb.INFO [2024-07-11 12:33:35.074][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-11 12:33:35.075][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-07-11 12:33:35.076][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-11 12:33:35.077][biodb::testContext]
biodb.INFO [2024-07-11 12:33:35.080][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-11 12:33:35.081][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-11 12:33:35.087][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:33:35.088][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-11 12:33:35.089][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-11 12:33:35.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.092][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.093][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-11 12:33:35.094][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-11 12:33:35.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.096][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.097][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-11 12:33:35.098][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-11 12:33:35.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.101][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-11 12:33:35.102][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-11 12:33:35.103][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-11 12:33:35.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.105][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[2024-07-11 12:33:35.106][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-11 12:33:35.106][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-11 12:33:35.107][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-11 12:33:35.108][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.109][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.110][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-11 12:33:35.111][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-11 12:33:35.112][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.114][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-11 12:33:35.115][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-11 12:33:35.116][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-11 12:33:35.117][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.119][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-11 12:33:35.120][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-11 12:33:35.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.122][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[2024-07-11 12:33:35.123][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-11 12:33:35.124][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-11 12:33:35.124][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-11 12:33:35.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.127][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.127][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-11 12:33:35.128][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-11 12:33:35.129][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-11 12:33:35.130][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-11 12:33:35.131][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-11 12:33:35.132][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-11 12:33:35.132][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.135][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-11 12:33:35.136][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-11 12:33:35.137][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.138][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.139][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-11 12:33:35.140][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-11 12:33:35.141][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.142][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.143][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-11 12:33:35.144][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-11 12:33:35.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.147][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-11 12:33:35.148][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-11 12:33:35.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.150][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.151][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-11 12:33:35.152][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-11 12:33:35.153][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.155][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-11 12:33:35.156][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-11 12:33:35.172][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-11 12:33:35.173][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.176][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-11 12:33:35.177][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-11 12:33:35.178][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-11 12:33:35.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.181][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-11 12:33:35.183][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.184][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-11 12:33:35.185][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.186][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:35.187][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.188][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.188][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.189][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.190][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:33:35.191][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:35.192][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.193][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-11 12:33:35.194][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:35.194][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.195][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.196][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:33:35.196][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:33:35.196][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-11 12:33:35.196][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-11 12:33:35.196][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-11 12:33:35.197][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:35.198][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.199][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.200][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:35.201][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.201][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.202][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.203][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.204][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:35.205][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:35.205][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.206][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.207][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-11 12:33:35.209][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.210][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-11 12:33:35.211][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.212][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:35.213][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.214][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.214][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.215][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.216][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-11 12:33:35.217][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:35.218][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.219][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-11 12:33:35.220][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:35.221][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.221][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.222][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:33:35.222][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:33:35.222][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-11 12:33:35.222][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-11 12:33:35.222][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-11 12:33:35.223][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:35.224][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.225][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.226][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:35.227][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.227][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.228][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.229][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.230][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:35.231][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:35.232][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.232][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.234][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-11 12:33:35.235][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.236][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-11 12:33:35.237][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.238][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:35.239][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.240][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.241][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.242][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.243][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:33:35.244][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:35.245][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.245][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-11 12:33:35.246][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:35.247][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.248][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.249][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.250][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:35.251][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.251][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.252][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:35.253][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.254][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.255][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.256][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.256][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:35.275][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:35.276][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.276][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.277][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-11 12:33:35.279][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.280][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-11 12:33:35.281][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.282][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:35.282][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.283][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.284][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.285][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.285][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-11 12:33:35.286][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:35.287][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.288][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-11 12:33:35.289][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:35.289][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.290][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.291][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.292][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:35.292][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.293][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.294][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:35.295][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.295][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.296][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.297][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.297][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:35.298][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:35.299][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.300][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.301][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:33:35.301][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.303][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.304][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.306][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[2024-07-11 12:33:35.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.309][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.310][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.312][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.313][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.314][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.316][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[2024-07-11 12:33:35.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.317][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.318][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.319][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.319][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[2024-07-11 12:33:35.320][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.326][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.327][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.329][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.330][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.332][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.333][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.334][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.334][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.335][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.338][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.340][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.344][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.346][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.348][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.350][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[2024-07-11 12:33:35.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.352][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.355][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.355][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.357][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.358][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.359][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.359][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.361][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.362][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-11 12:33:35.363][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-11 12:33:35.364][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-11 12:33:35.365][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-11 12:33:35.366][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-11 12:33:35.368][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-11 12:33:35.369][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-11 12:33:35.370][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-11 12:33:35.371][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-11 12:33:35.372][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-11 12:33:35.374][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-11 12:33:35.375][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-11 12:33:35.376][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-11 12:33:35.377][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-11 12:33:35.378][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-11 12:33:35.379][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-11 12:33:35.380][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-11 12:33:35.382][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-11 12:33:35.383][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-11 12:33:35.384][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-11 12:33:35.385][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-11 12:33:35.387][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-11 12:33:35.388][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-11 12:33:35.389][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-11 12:33:35.390][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-11 12:33:35.392][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-11 12:33:35.393][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-11 12:33:35.394][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-11 12:33:35.395][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-11 12:33:35.396][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-11 12:33:35.398][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-11 12:33:35.399][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-11 12:33:35.400][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-11 12:33:35.401][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-11 12:33:35.402][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-11 12:33:35.403][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-11 12:33:35.404][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-11 12:33:35.406][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-11 12:33:35.407][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-11 12:33:35.408][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-11 12:33:35.409][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-11 12:33:35.410][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-11 12:33:35.411][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-11 12:33:35.413][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-11 12:33:35.414][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-11 12:33:35.415][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-11 12:33:35.416][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-11 12:33:35.417][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-11 12:33:35.418][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-11 12:33:35.420][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-11 12:33:35.421][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-11 12:33:35.422][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-11 12:33:35.423][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-11 12:33:35.424][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-11 12:33:35.425][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-11 12:33:35.426][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-11 12:33:35.427][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-11 12:33:35.428][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-11 12:33:35.429][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-11 12:33:35.431][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-11 12:33:35.432][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-11 12:33:35.433][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-11 12:33:35.434][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-11 12:33:35.435][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-11 12:33:35.436][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-11 12:33:35.437][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-11 12:33:35.438][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-11 12:33:35.440][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-11 12:33:35.441][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-11 12:33:35.442][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-11 12:33:35.443][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-11 12:33:35.444][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-11 12:33:35.445][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-11 12:33:35.446][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-11 12:33:35.447][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-11 12:33:35.448][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-11 12:33:35.450][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-11 12:33:35.451][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-11 12:33:35.452][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-11 12:33:35.453][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-11 12:33:35.454][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-11 12:33:35.455][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-11 12:33:35.456][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-11 12:33:35.457][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-11 12:33:35.459][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-11 12:33:35.460][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:33:35.461][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.462][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.462][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.464][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.465][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.466][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.467][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.468][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.470][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.471][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.471][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.472][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.473][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.475][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.476][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.478][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.478][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.479][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.480][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.498][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.499][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.500][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.501][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.501][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.502][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[2024-07-11 12:33:35.503][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.506][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.506][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.508][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.509][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.510][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.512][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.513][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.514][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.515][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.516][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.517][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.518][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.518][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.522][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.523][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.523][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.524][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.525][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.525][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.527][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.529][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.532][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.534][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.537][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.538][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.539][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.540][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.540][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.541][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.542][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.542][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.543][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.545][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.546][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.548][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.548][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.550][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.550][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.551][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.552][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.553][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.554][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:35.555][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:35.556][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:35.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:35.557][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:35.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:35.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:35.560][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-11 12:33:35.570][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:33:35.572][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.573][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.574][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.574][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:35.575][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.576][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.577][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.577][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.578][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:33:35.579][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:35.580][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.581][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-11 12:33:35.581][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-11 12:33:35.582][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-11 12:33:35.583][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:35.584][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:33:35.584][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:33:35.585][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:35.586][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.587][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:35.588][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:35.589][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:35.589][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:35.590][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-11 12:33:35.590][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-11 12:33:35.591][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:35.592][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:35.592][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:35.593][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:35.594][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-11 12:33:35.595][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-11 12:33:35.599][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:33:35.599][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-11 12:33:35.600][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:33:35.602][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-11 12:33:35.603][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-11 12:33:35.604][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-11 12:33:35.605][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-11 12:33:35.605][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-11 12:33:35.607][biodb::testThat]
biodb.INFO [2024-07-11 12:33:35.608][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-07-11 12:33:35.609][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:35.609][biodb::testThat]
biodb.DEBUG[2024-07-11 12:33:35.613][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[2024-07-11 12:33:35.617][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:35.618][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:33:35.619][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-07-11 12:33:35.932][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-07-11 12:33:36.229][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:36.232][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-07-11 12:33:36.236][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-07-11 12:33:36.246][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-07-11 12:33:36.249][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:36.250][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:36.251][rule$waitAsNeeded] Wait 0.367348 second(s).
biodb.TRACE[2024-07-11 12:33:36.771][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-07-11 12:33:37.083][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2024-07-11 12:33:37.390][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:37.392][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-07-11 12:33:37.396][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-07-11 12:33:37.407][biodb::testThat]
biodb.INFO [2024-07-11 12:33:37.408][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-07-11 12:33:37.409][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:37.409][biodb::testThat]
biodb.INFO [2024-07-11 12:33:37.436][biodb::testThat]
biodb.INFO [2024-07-11 12:33:37.438][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-07-11 12:33:37.438][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:37.439][biodb::testThat]
biodb.DEBUG[2024-07-11 12:33:37.442][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-07-11 12:33:37.445][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:37.446][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:37.447][rule$waitAsNeeded] Wait 0.322719 second(s).
biodb.TRACE[2024-07-11 12:33:37.922][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-07-11 12:33:38.073][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-07-11 12:33:38.222][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:38.224][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-07-11 12:33:38.229][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-07-11 12:33:38.234][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-07-11 12:33:38.238][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-11 12:33:38.239][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-07-11 12:33:38.240][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:33:38.241][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-07-11 12:33:38.247][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-07-11 12:33:38.251][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:38.267][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:38.276][rule$waitAsNeeded] Wait 0.6451 second(s).
biodb.TRACE[2024-07-11 12:33:38.986][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-07-11 12:33:39.129][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2024-07-11 12:33:39.266][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:39.268][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-07-11 12:33:39.272][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-07-11 12:33:39.280][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2024-07-11 12:33:39.283][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:39.284][private$doSendRequestLoop] Request body is "".
biodb.DEBUG[2024-07-11 12:33:39.285][rule$waitAsNeeded] Wait 0.700197 second(s).
biodb.TRACE[2024-07-11 12:33:40.137][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-07-11 12:33:41.067][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-07-11 12:33:42.124][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:42.127][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-07-11 12:33:42.132][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-07-11 12:33:42.312][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-07-11 12:33:42.315][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-07-11 12:33:42.316][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-07-11 12:33:42.318][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2024-07-11 12:33:43.227][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2024-07-11 12:33:44.281][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-07-11 12:33:44.284][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-07-11 12:33:44.290][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-07-11 12:33:44.510][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-11 12:33:44.511][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-11 12:33:44.512][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-11 12:33:44.513][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-11 12:33:44.514][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.515][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.516][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.517][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.517][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-07-11 12:33:44.522][biodb::testContext]
biodb.INFO [2024-07-11 12:33:44.523][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-11 12:33:44.524][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-07-11 12:33:44.525][biodb::testContext] ********************************************************************************
biodb.INFO [2024-07-11 12:33:44.526][biodb::testContext]
biodb.INFO [2024-07-11 12:33:44.529][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.12.0.
biodb.DEBUG[2024-07-11 12:33:44.531][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-07-11 12:33:44.536][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:33:44.537][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-07-11 12:33:44.538][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-07-11 12:33:44.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.541][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-07-11 12:33:44.542][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-07-11 12:33:44.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.544][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.545][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-07-11 12:33:44.546][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-07-11 12:33:44.547][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.547][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.548][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.549][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-07-11 12:33:44.550][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-07-11 12:33:44.551][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-07-11 12:33:44.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.553][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.553][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-07-11 12:33:44.554][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-07-11 12:33:44.555][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-07-11 12:33:44.556][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.556][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.557][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.558][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-07-11 12:33:44.559][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-07-11 12:33:44.560][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.560][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.561][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.562][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-07-11 12:33:44.563][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-07-11 12:33:44.564][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-07-11 12:33:44.564][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.565][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.566][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.567][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-07-11 12:33:44.567][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-07-11 12:33:44.568][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.569][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.570][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.571][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-07-11 12:33:44.572][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-07-11 12:33:44.573][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-07-11 12:33:44.574][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.575][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.576][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.576][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-07-11 12:33:44.577][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-07-11 12:33:44.578][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-07-11 12:33:44.579][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-07-11 12:33:44.580][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-07-11 12:33:44.581][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-07-11 12:33:44.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.582][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.583][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.584][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-07-11 12:33:44.585][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-07-11 12:33:44.585][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.586][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.588][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-07-11 12:33:44.588][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-07-11 12:33:44.589][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.590][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.591][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.591][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-07-11 12:33:44.592][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-07-11 12:33:44.593][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.594][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.594][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.595][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-07-11 12:33:44.596][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-07-11 12:33:44.597][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.598][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.599][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-07-11 12:33:44.600][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-07-11 12:33:44.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.602][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.602][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-07-11 12:33:44.603][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-07-11 12:33:44.619][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-07-11 12:33:44.621][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.622][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[2024-07-11 12:33:44.623][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-07-11 12:33:44.624][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-07-11 12:33:44.625][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-07-11 12:33:44.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.627][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.628][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-07-11 12:33:44.630][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.631][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-07-11 12:33:44.631][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.632][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:44.633][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.634][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.635][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.635][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.636][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:33:44.637][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:44.638][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.639][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-07-11 12:33:44.639][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:44.640][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.641][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.642][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:33:44.642][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:33:44.642][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-11 12:33:44.642][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-11 12:33:44.642][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-11 12:33:44.643][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:44.643][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.644][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.645][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:44.645][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.646][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.647][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.648][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.648][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:44.649][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:44.650][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.651][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.652][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-07-11 12:33:44.653][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.654][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-07-11 12:33:44.655][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.656][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:44.657][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.658][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.658][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.659][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.660][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-11 12:33:44.661][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:44.661][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.662][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-07-11 12:33:44.663][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:44.664][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.665][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.665][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:33:44.665][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:33:44.665][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-07-11 12:33:44.665][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-07-11 12:33:44.665][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-07-11 12:33:44.666][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:44.667][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.668][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.668][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:44.669][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.670][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.671][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.671][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.672][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:44.673][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:44.673][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.674][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.675][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-07-11 12:33:44.677][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.678][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-07-11 12:33:44.678][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.679][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:44.680][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.681][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.681][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.682][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.683][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:33:44.684][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:44.685][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.685][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-07-11 12:33:44.686][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:44.687][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.688][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.688][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.689][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:44.690][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.691][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.691][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:44.692][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.693][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.694][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.694][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.695][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:44.696][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:44.696][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.697][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.698][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-07-11 12:33:44.700][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.700][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-07-11 12:33:44.701][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.702][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:44.703][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.704][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.704][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.705][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.706][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-07-11 12:33:44.707][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:44.708][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.709][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-07-11 12:33:44.710][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:44.710][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.712][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.713][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.714][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:44.715][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.716][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.716][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:44.717][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.718][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.719][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.720][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:44.720][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:44.721][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.722][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.723][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:33:44.723][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.724][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.726][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.727][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[2024-07-11 12:33:44.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.731][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.732][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.736][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.737][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.738][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[2024-07-11 12:33:44.739][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.742][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.757][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.760][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.761][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.761][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.762][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.763][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.763][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.764][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.764][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.765][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.766][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.768][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.769][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.771][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.772][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.773][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[2024-07-11 12:33:44.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.774][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.776][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.777][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.778][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-07-11 12:33:44.778][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-07-11 12:33:44.779][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-07-11 12:33:44.780][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-07-11 12:33:44.780][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-07-11 12:33:44.781][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-07-11 12:33:44.781][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-07-11 12:33:44.782][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-07-11 12:33:44.782][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-07-11 12:33:44.783][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-07-11 12:33:44.783][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-07-11 12:33:44.784][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-07-11 12:33:44.784][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-07-11 12:33:44.785][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-07-11 12:33:44.785][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-07-11 12:33:44.786][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-11 12:33:44.787][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-07-11 12:33:44.787][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-07-11 12:33:44.788][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-07-11 12:33:44.788][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-07-11 12:33:44.789][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-07-11 12:33:44.789][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-07-11 12:33:44.790][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-07-11 12:33:44.790][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-07-11 12:33:44.791][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-07-11 12:33:44.791][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-07-11 12:33:44.792][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-07-11 12:33:44.792][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-07-11 12:33:44.793][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-07-11 12:33:44.793][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-07-11 12:33:44.794][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-07-11 12:33:44.794][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-07-11 12:33:44.795][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-07-11 12:33:44.795][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-07-11 12:33:44.796][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-07-11 12:33:44.796][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-07-11 12:33:44.797][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-07-11 12:33:44.797][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-07-11 12:33:44.798][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-07-11 12:33:44.798][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-07-11 12:33:44.799][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-07-11 12:33:44.799][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-07-11 12:33:44.800][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-07-11 12:33:44.800][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-07-11 12:33:44.801][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-07-11 12:33:44.801][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-07-11 12:33:44.802][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-07-11 12:33:44.802][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-07-11 12:33:44.803][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-07-11 12:33:44.803][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-07-11 12:33:44.804][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-07-11 12:33:44.804][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-07-11 12:33:44.805][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-07-11 12:33:44.805][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-07-11 12:33:44.806][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-07-11 12:33:44.806][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-07-11 12:33:44.807][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-07-11 12:33:44.807][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-07-11 12:33:44.808][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-07-11 12:33:44.808][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-07-11 12:33:44.809][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-07-11 12:33:44.809][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-07-11 12:33:44.810][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-07-11 12:33:44.810][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-07-11 12:33:44.811][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-07-11 12:33:44.811][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-07-11 12:33:44.812][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-07-11 12:33:44.812][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-07-11 12:33:44.813][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-07-11 12:33:44.813][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-07-11 12:33:44.814][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-07-11 12:33:44.814][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-07-11 12:33:44.815][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-07-11 12:33:44.815][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-07-11 12:33:44.815][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-07-11 12:33:44.816][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-07-11 12:33:44.816][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-07-11 12:33:44.817][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-07-11 12:33:44.817][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-07-11 12:33:44.818][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-07-11 12:33:44.818][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-07-11 12:33:44.819][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-07-11 12:33:44.819][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-07-11 12:33:44.820][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-07-11 12:33:44.821][initialize] This is biodb version 1.12.0.
biodb.DEBUG[2024-07-11 12:33:44.821][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-07-11 12:33:44.821][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.822][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.822][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.823][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.824][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.826][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.827][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.828][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.829][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.830][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.830][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.832][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.835][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.836][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.837][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.839][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.841][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.842][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.843][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.843][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.846][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.848][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.850][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.852][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.853][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.855][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.856][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.860][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.863][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.864][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.865][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.867][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.868][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.869][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.871][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.872][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.872][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.873][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.874][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.875][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.877][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.877][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.877][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.878][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.878][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.878][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.879][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.880][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.880][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.880][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.896][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.903][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.904][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.904][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.905][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.906][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.906][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.907][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.908][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.908][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.909][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.909][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-07-11 12:33:44.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:44.910][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:44.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:44.911][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:44.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:44.911][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-07-11 12:33:44.912][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-07-11 12:33:44.914][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:33:44.915][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.916][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.916][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.916][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-07-11 12:33:44.917][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.917][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.917][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.918][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.918][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-07-11 12:33:44.918][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-07-11 12:33:44.919][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.919][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-07-11 12:33:44.919][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-07-11 12:33:44.920][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-07-11 12:33:44.921][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-07-11 12:33:44.921][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.922][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.923][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-07-11 12:33:44.924][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-07-11 12:33:44.925][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-07-11 12:33:44.926][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-07-11 12:33:44.927][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-07-11 12:33:44.927][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-07-11 12:33:44.927][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-07-11 12:33:44.928][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-07-11 12:33:44.929][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-07-11 12:33:44.930][self$setPropertyValue]
biodb.DEBUG[2024-07-11 12:33:44.931][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-07-11 12:33:44.932][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-07-11 12:33:44.933][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:33:44.934][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-07-11 12:33:44.934][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-07-11 12:33:44.935][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-07-11 12:33:44.935][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-11 12:33:44.936][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-07-11 12:33:44.936][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-07-11 12:33:44.937][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-07-11 12:33:44.937][biodb::testThat]
biodb.INFO [2024-07-11 12:33:44.938][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-07-11 12:33:44.938][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-07-11 12:33:44.938][biodb::testThat]
biodb.DEBUG[2024-07-11 12:33:44.941][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[2024-07-11 12:33:44.943][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-07-11 12:33:44.944][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-07-11 12:33:44.945][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-07-11 12:33:44.978][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-07-11 12:33:46.197][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-07-11 12:33:46.198][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-07-11 12:33:46.200][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-07-11 12:33:46.201][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2024-07-11 12:33:46.203][loadFileContents] Loaded 2 files from cache: [2]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-07-11 12:33:46.204][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-07-11 12:33:46.205][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-07-11 12:33:46.206][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-07-11 12:33:46.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:46.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:46.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:46.215][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:46.216][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:46.217][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:46.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:46.222][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.226][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.229][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.233][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.234][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.236][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:33:46.237][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:33:46.238][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.239][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.240][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:33:46.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:33:46.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.243][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.246][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.250][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.251][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.253][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.255][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.256][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:33:46.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.260][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:33:46.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.263][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.267][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.270][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.274][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.277][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.279][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:33:46.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.282][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-11 12:33:46.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.285][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.288][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.292][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:33:46.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.295][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.298][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.302][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.306][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.307][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.309][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.313][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.316][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.323][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.327][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.330][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.331][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.332][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.333][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.336][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:33:46.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:46.337][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:46.338][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:46.344][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:46.345][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:46.346][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:46.347][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:46.351][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.353][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.355][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.359][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.363][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.366][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:33:46.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-07-11 12:33:46.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.370][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:33:46.371][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-07-11 12:33:46.372][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.374][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.376][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.377][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.378][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.381][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.385][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.388][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:33:46.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.392][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-07-11 12:33:46.392][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.395][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.397][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.398][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.399][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.408][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:33:46.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.411][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-07-11 12:33:46.412][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.414][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.418][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.419][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.421][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-07-11 12:33:46.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.424][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.428][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.430][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.467][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.472][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.475][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.479][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.482][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.485][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.487][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.488][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.492][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.493][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.494][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.495][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.497][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.497][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.498][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-07-11 12:33:46.505][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2024-07-11 12:33:46.508][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-07-11 12:33:46.510][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:46.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:46.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:46.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:46.519][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:46.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:46.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:46.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.529][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-11 12:33:46.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-11 12:33:46.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.532][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-11 12:33:46.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-11 12:33:46.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.536][private$selectFields] Fields none
biodb.TRACE[2024-07-11 12:33:46.537][private$selectFields]
biodb.TRACE[2024-07-11 12:33:46.537][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-07-11 12:33:46.538][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:33:46.539][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:33:46.540][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.540][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.541][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.542][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.543][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.544][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.545][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.546][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.547][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.548][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.549][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.550][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.551][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.552][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.552][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.553][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.554][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.555][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.556][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.556][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.557][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.558][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.559][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.560][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.560][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.561][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.562][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.563][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.564][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.564][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.565][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.566][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.567][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.568][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.568][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.569][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.570][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.571][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.571][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.572][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.573][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.574][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.575][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.575][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.576][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.577][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.578][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.579][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.580][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.581][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.581][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.582][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.583][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.584][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.585][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.585][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.586][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.587][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.588][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.588][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.589][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.590][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.591][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.592][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.593][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:33:46.593][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:33:46.594][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.595][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.596][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.597][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.597][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.598][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.599][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.600][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.600][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.601][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.602][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.603][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.603][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.604][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.605][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.606][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.606][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.607][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.608][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.609][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.610][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.611][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.612][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.613][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.615][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.616][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.617][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.618][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.619][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.620][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.621][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.621][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.622][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-07-11 12:33:46.623][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.627][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.627][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.628][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.633][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.636][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.640][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.643][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.646][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.649][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.653][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.656][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.660][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.661][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.663][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.665][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.666][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.670][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.673][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.677][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.680][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.684][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.688][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.691][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.695][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.698][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.699][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.702][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.723][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2024-07-11 12:33:46.725][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-07-11 12:33:46.726][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:46.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:46.732][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:46.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:46.734][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:46.734][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-07-11 12:33:46.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.740][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-07-11 12:33:46.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.743][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-07-11 12:33:46.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-07-11 12:33:46.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.746][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-07-11 12:33:46.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-07-11 12:33:46.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.749][private$selectFields] Fields none
biodb.TRACE[2024-07-11 12:33:46.750][private$selectFields]
biodb.TRACE[2024-07-11 12:33:46.751][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-07-11 12:33:46.753][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-07-11 12:33:46.754][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:33:46.755][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.756][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.756][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.757][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.758][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.759][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.759][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.760][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.761][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.762][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.763][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.764][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.765][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.766][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.767][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.768][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.769][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.771][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.772][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.773][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.774][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.775][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.776][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.777][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.778][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.779][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.780][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.781][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.781][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.782][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.783][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.784][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.785][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.787][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.787][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.788][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.789][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.790][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.791][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.791][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.792][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.793][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.794][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.794][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.795][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.796][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.797][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.798][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.798][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.799][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.800][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.801][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.802][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.802][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.803][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.804][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.805][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.806][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.806][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.807][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.808][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.809][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.809][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.810][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:33:46.811][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-07-11 12:33:46.812][ef$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.813][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.814][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.814][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.815][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.816][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.817][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.818][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.819][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.820][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.821][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.821][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.822][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.823][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.824][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.825][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.825][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.826][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.827][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.828][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.829][ef$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.830][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.830][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.831][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.832][ef$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.833][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.834][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.834][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.835][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.836][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.837][ef$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.837][ef$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.838][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2024-07-11 12:33:46.839][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.842][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.843][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.844][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.845][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.846][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-07-11 12:33:46.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-07-11 12:33:46.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.849][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.852][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.856][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-07-11 12:33:46.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.859][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.862][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.865][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.865][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-07-11 12:33:46.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.869][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.871][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.875][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.879][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-07-11 12:33:46.880][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.881][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.882][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.886][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.886][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.887][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.889][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-07-11 12:33:46.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.892][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.895][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.899][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-07-11 12:33:46.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-07-11 12:33:46.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.902][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.908][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-07-11 12:33:46.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-07-11 12:33:46.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.916][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.919][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.920][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-07-11 12:33:46.921][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-07-11 12:33:46.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-07-11 12:33:46.926][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-07-11 12:33:46.927][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-07-11 12:33:46.928][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-07-11 12:33:46.934][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-07-11 12:33:46.935][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-07-11 12:33:46.936][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-07-11 12:33:46.937][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-07-11 12:33:46.938][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-07-11 12:33:46.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-07-11 12:33:46.939][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-07-11 12:33:46.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-07-11 12:33:46.941][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-07-11 12:33:46.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 166 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── 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 2 | WARN 0 | SKIP 0 | PASS 166 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 2.423 | 0.648 | 3.863 | |
| LipidmapsStructureEntry | 0.456 | 0.015 | 0.472 | |