| Back to Multiple platform build/check report for BioC 3.18: simplified long |
|
This page was generated on 2024-03-04 11:37:10 -0500 (Mon, 04 Mar 2024).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) | x86_64 | 4.3.2 Patched (2023-11-13 r85521) -- "Eye Holes" | 4692 |
| palomino4 | Windows Server 2022 Datacenter | x64 | 4.3.2 (2023-10-31 ucrt) -- "Eye Holes" | 4445 |
| lconway | macOS 12.7.1 Monterey | x86_64 | 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes" | 4466 |
| Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X | ||||
| Package 200/2266 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.8.0 (landing page) Pierrick Roger
| nebbiolo2 | Linux (Ubuntu 22.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
| palomino4 | Windows Server 2022 Datacenter / x64 | OK | OK | ERROR | OK | |||||||||
| lconway | macOS 12.7.1 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
| kjohnson1 | macOS 13.6.1 Ventura / arm64 | see weekly results here | ||||||||||||
|
To the developers/maintainers of the biodbLipidmaps package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
| Package: biodbLipidmaps |
| Version: 1.8.0 |
| Command: /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_1.8.0.tar.gz |
| StartedAt: 2024-03-03 19:14:18 -0500 (Sun, 03 Mar 2024) |
| EndedAt: 2024-03-03 19:17:43 -0500 (Sun, 03 Mar 2024) |
| EllapsedTime: 205.0 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_1.8.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/Users/biocbuild/bbs-3.18-bioc/meat/biodbLipidmaps.Rcheck’
* using R version 4.3.2 Patched (2023-11-01 r85457)
* using platform: x86_64-apple-darwin20 (64-bit)
* R was compiled by
Apple clang version 14.0.3 (clang-1403.0.22.14.1)
GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.7.1
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.8.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
── Failure ('test_100_generic.R:16:1'): The peak table is correct. ─────────────
any(vapply(entries, is.null, FUN.VALUE = TRUE)) is not FALSE
`actual`: TRUE
`expected`: FALSE
One of the entries is NULL.
Backtrace:
▆
1. ├─base::do.call(fct, params)
2. └─biodb (local) `<fn>`(conn = `<LpdmpsSC>`, opt = `<named list>`)
3. └─testthat::expect_false(...)
[ FAIL 2 | WARN 0 | SKIP 0 | PASS 167 ]
Error: Test failures
Execution halted
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE
Status: 1 ERROR
See
‘/Users/biocbuild/bbs-3.18-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/4.3-x86_64/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 ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (biodbLipidmaps)
biodbLipidmaps.Rcheck/tests/testthat.Rout.fail
R version 4.3.2 Patched (2023-11-01 r85457) -- "Eye Holes"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin20 (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> # Script needed to run testthat automatically from ‘R CMD check’. See
> # testthat::test_dir documentation.
> library(testthat)
> library(biodbLipidmaps)
> Sys.setenv(TESTTHAT_REPORTER="summary")
> Sys.setenv(BIODB_LOG_DST="console")
> test_check("biodbLipidmaps")
biodb.INFO [2024-03-03 19:15:16.329][biodb::testContext]
biodb.INFO [2024-03-03 19:15:16.334][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-03 19:15:16.336][biodb::testContext] Test context - Generic tests
biodb.INFO [2024-03-03 19:15:16.337][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-03 19:15:16.339][biodb::testContext]
biodb.INFO [2024-03-03 19:15:16.349][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-03 19:15:16.352][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-03 19:15:16.363][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:15:16.364][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-03 19:15:16.366][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-03 19:15:16.368][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.369][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.372][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-03 19:15:16.397][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-03 19:15:16.399][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.403][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-03 19:15:16.405][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-03 19:15:16.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.409][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.410][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-03 19:15:16.411][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-03 19:15:16.412][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-03 19:15:16.413][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.415][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.416][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-03 19:15:16.417][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-03 19:15:16.419][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-03 19:15:16.419][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.420][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.422][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.423][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-03 19:15:16.425][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-03 19:15:16.426][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.429][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.430][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-03 19:15:16.432][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-03 19:15:16.434][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-03 19:15:16.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.439][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-03 19:15:16.441][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-03 19:15:16.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.444][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.446][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-03 19:15:16.447][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-03 19:15:16.448][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-03 19:15:16.449][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.450][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.451][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.452][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-03 19:15:16.454][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-03 19:15:16.456][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-03 19:15:16.457][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-03 19:15:16.458][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-03 19:15:16.459][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-03 19:15:16.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.461][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.463][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[2024-03-03 19:15:16.464][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-03 19:15:16.466][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-03 19:15:16.467][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.470][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-03 19:15:16.472][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-03 19:15:16.474][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.475][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.476][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.477][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-03 19:15:16.478][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-03 19:15:16.480][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.482][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.483][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.484][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-03 19:15:16.485][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-03 19:15:16.486][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.488][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.489][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-03 19:15:16.490][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-03 19:15:16.492][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.494][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.496][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-03 19:15:16.497][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-03 19:15:16.526][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-03 19:15:16.529][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.530][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.531][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.532][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-03 19:15:16.533][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-03 19:15:16.535][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-03 19:15:16.536][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.539][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.543][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-03 19:15:16.590][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.620][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-03 19:15:16.622][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.623][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:15:16.625][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.626][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.627][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.628][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.630][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:15:16.631][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:15:16.632][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.634][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-03 19:15:16.635][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:15:16.636][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.638][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.639][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:15:16.639][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:15:16.639][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-03 19:15:16.639][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-03 19:15:16.639][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-03 19:15:16.641][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:15:16.642][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.643][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.643][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:15:16.644][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.645][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.646][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.648][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.649][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:15:16.649][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:15:16.650][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.652][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.653][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-03 19:15:16.656][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.657][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-03 19:15:16.659][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.660][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:15:16.662][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.663][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.664][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.665][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.667][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-03 19:15:16.668][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:15:16.669][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.670][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-03 19:15:16.671][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:15:16.672][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.673][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.674][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:15:16.674][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:15:16.674][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-03 19:15:16.674][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-03 19:15:16.674][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-03 19:15:16.675][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:15:16.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.678][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:15:16.679][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.681][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.682][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.683][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.684][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:15:16.685][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:15:16.686][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.687][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.688][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-03 19:15:16.690][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.692][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-03 19:15:16.693][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.695][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:15:16.696][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.699][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.700][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.701][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:15:16.703][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:15:16.704][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.705][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-03 19:15:16.706][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:15:16.708][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.709][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.710][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.712][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:15:16.713][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.714][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.715][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:15:16.716][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.717][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.718][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.720][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.721][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:15:16.722][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:15:16.723][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.724][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.726][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-03 19:15:16.727][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.729][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-03 19:15:16.730][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.732][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:15:16.733][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.735][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.737][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.738][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.740][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-03 19:15:16.741][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:15:16.742][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.744][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-03 19:15:16.745][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:15:16.746][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.748][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:16.749][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.750][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:15:16.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.754][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:15:16.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:16.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:16.758][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:15:16.759][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.760][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:15:16.760][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:15:16.761][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:16.762][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:16.766][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:15:16.768][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.781][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.783][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.786][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.787][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.790][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.792][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.793][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.796][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.797][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.798][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.803][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.815][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.821][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.824][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.836][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[2024-03-03 19:15:16.837][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.839][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.840][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.841][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.842][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.844][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.845][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.847][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.848][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.850][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.851][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.852][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[2024-03-03 19:15:16.853][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.854][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.856][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.858][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:16.859][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:16.860][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:16.861][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:16.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:16.864][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[2024-03-03 19:15:16.865][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-03 19:15:16.872][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-03 19:15:16.875][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-03 19:15:16.877][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-03 19:15:16.879][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-03 19:15:16.881][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-03 19:15:16.883][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-03 19:15:16.886][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-03 19:15:16.888][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-03 19:15:16.890][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-03 19:15:16.892][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-03 19:15:16.894][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-03 19:15:16.896][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-03 19:15:16.898][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-03 19:15:16.900][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-03 19:15:16.902][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-03 19:15:16.904][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-03 19:15:16.906][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-03 19:15:16.908][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-03 19:15:16.917][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-03 19:15:16.919][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-03 19:15:16.921][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-03 19:15:16.923][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-03 19:15:16.925][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-03 19:15:16.927][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-03 19:15:16.929][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-03 19:15:16.931][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-03 19:15:16.933][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-03 19:15:16.935][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-03 19:15:16.936][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-03 19:15:16.938][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-03 19:15:16.940][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-03 19:15:16.941][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-03 19:15:16.943][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-03 19:15:16.945][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-03 19:15:16.947][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-03 19:15:16.949][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-03 19:15:16.951][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-03 19:15:16.953][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-03 19:15:16.954][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-03 19:15:16.956][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-03 19:15:16.958][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-03 19:15:16.959][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-03 19:15:16.961][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-03 19:15:16.962][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-03 19:15:16.963][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-03 19:15:16.965][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-03 19:15:16.966][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-03 19:15:16.968][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-03 19:15:16.970][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-03 19:15:16.971][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-03 19:15:16.972][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-03 19:15:16.973][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-03 19:15:16.975][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-03 19:15:16.977][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-03 19:15:16.978][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-03 19:15:16.980][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-03 19:15:16.981][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-03 19:15:16.983][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-03 19:15:16.984][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-03 19:15:16.986][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-03 19:15:16.988][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-03 19:15:16.990][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-03 19:15:16.992][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-03 19:15:16.993][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-03 19:15:16.995][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-03 19:15:16.996][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-03 19:15:16.998][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-03 19:15:16.999][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-03 19:15:17.001][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-03 19:15:17.002][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-03 19:15:17.003][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-03 19:15:17.004][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-03 19:15:17.006][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-03 19:15:17.008][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-03 19:15:17.010][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-03 19:15:17.012][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-03 19:15:17.013][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-03 19:15:17.015][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-03 19:15:17.017][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-03 19:15:17.018][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-03 19:15:17.019][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-03 19:15:17.020][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-03 19:15:17.026][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-03 19:15:17.029][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-03 19:15:17.032][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:15:17.033][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.033][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.034][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.035][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.041][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.043][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.044][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.048][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.049][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.051][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.057][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.058][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.060][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.061][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.062][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.063][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.064][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.066][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.067][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.074][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.075][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.078][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[2024-03-03 19:15:17.079][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.080][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.082][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.083][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.084][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.085][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.086][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[2024-03-03 19:15:17.087][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.089][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.090][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.098][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.100][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.102][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.103][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.105][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.106][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.107][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.111][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.112][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.113][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.114][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.115][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.116][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[2024-03-03 19:15:17.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.119][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.120][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.122][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[2024-03-03 19:15:17.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.132][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.135][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.137][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.139][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.139][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.141][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.142][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.143][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.145][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.149][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.156][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.157][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.159][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.161][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:15:17.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:17.172][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-03 19:15:17.181][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:15:17.184][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:17.185][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-03 19:15:17.187][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:17.188][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:15:17.190][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:17.191][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:15:17.192][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:17.194][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:15:17.195][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:15:17.196][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:15:17.204][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:17.206][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-03 19:15:17.207][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-03 19:15:17.209][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-03 19:15:17.210][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-03 19:15:17.211][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:15:17.211][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:15:17.212][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:15:17.213][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:17.214][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:17.215][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:15:17.216][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:15:17.218][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:15:17.219][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:15:17.220][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:15:17.220][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-03 19:15:17.221][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:15:17.222][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:15:17.223][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-03 19:15:17.224][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:15:17.232][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-03 19:15:17.234][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-03 19:15:17.262][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:15:17.263][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-03 19:15:17.267][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:15:17.271][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-03 19:15:17.275][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-03 19:15:17.276][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-03 19:15:17.278][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-03 19:15:17.279][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-03 19:15:17.291][biodb::testThat]
biodb.INFO [2024-03-03 19:15:17.292][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2024-03-03 19:15:17.293][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:17.294][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:17.300][loadFileContents] Loaded 1 files from cache: [1]: "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2024-03-03 19:15:17.302][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-03 19:15:17.308][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-03 19:15:17.319][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:17.320][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:17.321][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:17.342][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:17.343][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:17.344][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:17.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:17.358][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.364][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.383][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.386][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:15:17.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:15:17.389][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.392][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:17.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:17.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.396][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:17.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:17.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.402][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.403][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.404][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.405][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.439][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.441][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.445][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.446][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.447][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.450][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.451][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.452][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.453][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.455][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:17.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.456][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.458][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:17.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.462][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.468][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.469][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.472][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.473][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.476][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.477][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.478][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.479][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.480][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:17.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.485][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-03 19:15:17.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.489][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.494][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.496][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.498][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.499][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:17.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.502][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.503][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.537][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.538][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.539][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.540][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.541][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.543][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.543][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.544][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.581][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.583][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.588][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.591][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.594][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.598][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.600][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.601][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.602][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.603][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.604][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.605][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.606][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.607][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.608][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.612][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.617][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.621][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.623][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.624][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.625][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.626][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.628][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.629][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.630][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.631][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:17.634][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-03 19:15:17.636][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:15:17.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:15:17.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.639][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:15:17.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:15:17.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.643][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-03 19:15:17.644][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-03 19:15:17.645][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.648][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-03 19:15:17.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-03 19:15:17.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.693][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.695][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.696][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.697][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.704][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.709][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.714][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.715][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.716][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.717][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.719][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.727][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.728][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.729][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.731][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.735][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.739][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:17.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.754][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.766][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.767][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.768][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.769][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.771][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.772][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.773][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.774][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.775][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.776][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.777][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.793][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.798][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.801][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.804][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.805][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.806][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.807][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.808][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.810][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:17.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:17.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.825][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.832][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.838][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.843][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.844][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.845][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.847][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.848][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.868][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.876][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.877][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.878][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.879][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.880][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.895][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.899][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.902][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.906][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.907][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.909][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.910][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.910][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.911][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.927][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.933][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.937][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.942][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.943][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.944][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.944][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.945][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:17.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.948][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.960][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:17.961][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:17.962][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.963][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.969][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.971][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:17.972][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.973][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.980][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:17.981][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:17.982][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.983][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:17.990][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.991][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:17.992][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:17.993][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.000][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.001][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.003][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.004][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.010][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:18.011][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:18.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.013][ef$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:18.023][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.053][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2024-03-03 19:15:18.054][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.056][biodb::testThat]
biodb.DEBUG[2024-03-03 19:15:18.072][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2024-03-03 19:15:18.081][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-03 19:15:18.085][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2024-03-03 19:15:18.087][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:18.089][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2024-03-03 19:15:18.090][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-03 19:15:18.119][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-03 19:15:18.121][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-03 19:15:18.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:18.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:18.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:18.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:18.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:18.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:18.136][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:18.142][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.148][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.154][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:15:18.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:15:18.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.160][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:15:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:15:18.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.165][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:18.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:18.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.170][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:18.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:18.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.174][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:18.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:18.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.179][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:18.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:18.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.183][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:18.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:18.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.187][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:18.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:18.190][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.191][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.193][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:18.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:18.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.197][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:18.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:18.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.201][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:18.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:18.203][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.206][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:18.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:18.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.210][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.214][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.219][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:18.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.221][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.222][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.223][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-03 19:15:18.224][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.226][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.226][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.230][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.231][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.234][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.235][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:18.236][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.237][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.238][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.240][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.241][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.243][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.244][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.245][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.248][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.256][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.261][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.266][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:18.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:18.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.272][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:18.272][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:18.273][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.274][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.279][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:18.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:18.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.287][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.291][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.308][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.309][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.312][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:18.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:18.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:18.320][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2024-03-03 19:15:18.321][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2024-03-03 19:15:18.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2024-03-03 19:15:18.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.324][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.325][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2024-03-03 19:15:18.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2024-03-03 19:15:18.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.330][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2024-03-03 19:15:18.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2024-03-03 19:15:18.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:18.347][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.348][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2024-03-03 19:15:18.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.350][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:18.354][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.355][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.356][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.358][ef$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:18.359][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2024-03-03 19:15:18.396][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.401][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.405][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.408][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:18.413][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2024-03-03 19:15:18.419][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[2024-03-03 19:15:18.442][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:18.459][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-03 19:15:18.460][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:18.463][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-03 19:15:18.465][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2024-03-03 19:15:18.483][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:18.485][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:18.487][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.488][ef$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:18.494][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.495][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2024-03-03 19:15:18.497][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.497][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:18.529][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.533][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.534][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.535][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.536][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:18.537][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:18.664][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[2024-03-03 19:15:18.668][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:18.670][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-03 19:15:18.672][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:18.674][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2024-03-03 19:15:18.699][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.701][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2024-03-03 19:15:18.702][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.703][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:18.732][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.736][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.741][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-03 19:15:18.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-03 19:15:18.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.747][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-03 19:15:18.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-03 19:15:18.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.807][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.813][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:15:18.814][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.817][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-03 19:15:18.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-03 19:15:18.820][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.821][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:18.822][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-03 19:15:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-03 19:15:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:18.826][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:18.835][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.836][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2024-03-03 19:15:18.838][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.839][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.849][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.850][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2024-03-03 19:15:18.851][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.852][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.863][biodb::testThat]
biodb.INFO [2024-03-03 19:15:18.864][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2024-03-03 19:15:18.866][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:18.867][biodb::testThat]
biodb.DEBUG[2024-03-03 19:15:18.872][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2024-03-03 19:15:20.545][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2024-03-03 19:15:21.000][biodb::testThat]
biodb.INFO [2024-03-03 19:15:21.002][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2024-03-03 19:15:21.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:21.005][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:21.013][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:21.015][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:21.016][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.017][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.018][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.019][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.020][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.021][ef$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:21.023][biodb::testThat]
biodb.INFO [2024-03-03 19:15:21.024][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2024-03-03 19:15:21.025][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:21.026][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:21.044][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:21.046][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:21.047][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.050][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:21.051][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:21.052][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.054][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.055][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:21.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:21.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:21.165][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[2024-03-03 19:15:21.169][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:21.170][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-03 19:15:21.172][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:21.173][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2024-03-03 19:15:21.262][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[2024-03-03 19:15:21.267][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:21.269][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2024-03-03 19:15:21.271][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:21.273][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2024-03-03 19:15:21.294][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-03 19:15:21.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-03 19:15:21.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.298][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.308][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:21.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:21.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.322][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.326][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.328][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.333][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.336][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.338][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:21.345][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:21.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:21.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:21.360][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[2024-03-03 19:15:21.365][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:21.366][cch$loadFileContent] Trying to load 1 files from cache: [1]: "304383a7dc8c451be84009e31d831359".
biodb.TRACE[2024-03-03 19:15:21.367][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:21.427][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content".
biodb.DEBUG[2024-03-03 19:15:22.976][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[2024-03-03 19:15:22.981][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:22.983][cch$loadFileContent] Trying to load 1 files from cache: [1]: "7f71825f1888a7b29e4b8407502d21e3".
biodb.TRACE[2024-03-03 19:15:22.985][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:22.993][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content".
biodb.DEBUG[2024-03-03 19:15:23.029][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[2024-03-03 19:15:23.034][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:23.036][cch$loadFileContent] Trying to load 1 files from cache: [1]: "fd41c675dd237f33cdaafcbb15058c54".
biodb.TRACE[2024-03-03 19:15:23.038][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:23.043][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content".
biodb.TRACE[2024-03-03 19:15:23.075][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-03 19:15:23.077][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-03 19:15:23.078][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:23.094][biodb::testThat]
biodb.INFO [2024-03-03 19:15:23.096][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2024-03-03 19:15:23.097][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:23.098][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:23.102][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-03 19:15:23.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-03 19:15:23.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:23.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:23.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:23.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:23.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:23.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:23.122][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:23.127][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.129][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:23.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:23.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:23.137][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:23.138][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:23.139][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:23.148][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:23.150][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:23.151][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:23.152][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:23.156][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[2024-03-03 19:15:23.160][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:15:23.162][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2024-03-03 19:15:23.164][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:15:23.212][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2024-03-03 19:15:24.527][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2024-03-03 19:15:24.578][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-03 19:15:24.581][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.INFO [2024-03-03 19:15:24.582][self$getFolderPath] Create cache folder "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2024-03-03 19:15:24.584][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-03 19:15:24.585][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-03 19:15:24.586][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-03 19:15:24.587][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:15:24.588][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-03 19:15:24.589][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-03 19:15:24.606][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:24.607][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:24.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:24.615][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:24.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:24.618][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:24.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:24.620][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2024-03-03 19:15:24.623][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:15:24.625][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:15:24.626][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2024-03-03 19:15:25.610][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2024-03-03 19:15:26.240][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:15:26.243][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2024-03-03 19:15:26.260][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2024-03-03 19:15:26.263][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:26.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:26.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:26.273][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:26.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:26.305][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:26.310][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[2024-03-03 19:15:26.312][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2024-03-03 19:15:26.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:15:26.335][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:15:26.353][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2024-03-03 19:15:26.980][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2024-03-03 19:15:27.647][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:15:27.649][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2024-03-03 19:15:27.653][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2024-03-03 19:15:27.657][private$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[2024-03-03 19:15:27.659][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-03 19:15:27.661][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-03 19:15:27.662][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-03 19:15:27.664][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:27.665][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:27.666][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:27.683][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:27.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:27.685][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:27.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:27.691][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.692][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.693][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.694][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.701][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:15:27.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:15:27.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.706][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:15:27.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:15:27.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.708][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.710][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:27.711][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:27.712][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.713][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.714][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:27.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.719][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.723][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.728][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.729][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.730][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.730][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.732][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.736][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:27.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:27.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.740][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:27.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:27.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:27.746][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:27.747][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.748][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:27.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:27.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.751][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.753][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.757][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.780][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.781][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:27.782][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.785][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-03 19:15:27.786][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.788][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.791][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.792][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.793][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.796][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:27.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.800][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.808][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.813][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.817][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.821][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.824][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:27.831][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:27.833][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:27.834][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:27.842][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:27.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:27.844][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:27.846][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:27.850][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.861][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:15:27.863][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:15:27.864][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.865][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:27.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:15:27.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.870][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:27.872][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:15:27.873][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.874][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.874][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.879][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:15:27.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.884][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.888][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.889][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:15:27.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.895][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:27.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:27.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.899][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:15:27.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:27.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.904][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:27.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:27.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.908][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:15:27.909][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:15:27.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.913][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.935][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.936][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.937][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.939][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:27.940][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.941][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.942][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.943][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-03 19:15:27.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.965][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.970][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:15:27.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.975][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:15:27.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:15:27.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.979][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.980][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.987][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:27.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.994][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:27.996][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:27.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:27.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:27.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.011][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.016][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.021][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.025][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.040][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.044][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:15:28.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:15:28.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:28.048][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2024-03-03 19:15:28.061][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-03 19:15:28.063][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:28.064][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:28.065][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:28.072][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:28.074][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:28.075][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:28.076][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:28.078][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.082][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.087][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.088][private$selectFields]
biodb.TRACE[2024-03-03 19:15:28.089][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:15:28.091][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:15:28.092][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.094][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.095][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.097][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.098][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.099][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.102][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.103][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.104][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.106][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.107][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.108][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.111][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.112][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:15:28.113][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.118][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.123][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.161][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-03 19:15:28.162][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:28.164][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:28.164][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:28.172][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:28.173][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:28.175][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:28.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:28.178][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.180][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.181][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.182][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.183][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.189][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.190][private$selectFields]
biodb.TRACE[2024-03-03 19:15:28.191][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:15:28.192][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:15:28.193][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.194][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.196][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.197][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.198][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.199][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.200][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.201][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.203][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.203][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.204][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.206][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.207][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.207][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.209][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.210][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:15:28.211][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.212][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.213][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.214][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.215][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.216][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.219][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.222][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.223][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.224][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-03 19:15:28.226][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:28.227][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:28.228][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:28.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:28.237][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:28.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:28.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:28.240][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.245][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.246][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.247][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.251][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.252][private$selectFields]
biodb.TRACE[2024-03-03 19:15:28.253][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:15:28.254][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:15:28.255][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.256][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.258][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.259][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.260][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.261][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.262][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.264][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.265][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.266][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.267][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:28.268][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.269][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.269][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.270][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.271][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:15:28.272][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.276][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.279][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.280][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:28.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.284][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-03 19:15:28.284][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-03 19:15:28.285][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-03 19:15:28.298][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-03 19:15:28.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-03 19:15:28.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:28.309][biodb::testThat]
biodb.INFO [2024-03-03 19:15:28.311][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2024-03-03 19:15:28.312][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:28.314][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:28.318][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-03 19:15:28.338][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-03 19:15:28.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.341][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.343][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:28.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:28.346][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.349][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.354][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.355][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.359][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.360][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.361][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.362][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:28.379][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:28.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:28.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:28.460][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:28.461][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:28.463][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:28.470][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:28.472][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:28.474][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:28.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:28.479][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[2024-03-03 19:15:28.484][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:15:28.486][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:15:28.488][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2024-03-03 19:15:32.498][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2024-03-03 19:15:44.598][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:15:44.601][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2024-03-03 19:15:44.712][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2024-03-03 19:15:45.912][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-03 19:15:45.941][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:45.942][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:45.943][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:45.950][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:45.952][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:45.952][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:45.953][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:45.967][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:45.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:45.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:45.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:45.973][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:45.974][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:45.975][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:45.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:45.998][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.000][private$selectFields]
biodb.TRACE[2024-03-03 19:15:46.001][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:15:46.003][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:15:46.004][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.005][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.006][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.007][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.008][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.009][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.011][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.012][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.012][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.013][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.026][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.027][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.029][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.030][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.031][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.033][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:15:46.034][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.040][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.044][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.045][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.047][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.048][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.049][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.051][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-03 19:15:46.052][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:46.053][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:46.054][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:46.061][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:46.063][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:46.064][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:46.065][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:46.067][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.077][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.078][private$selectFields]
biodb.TRACE[2024-03-03 19:15:46.079][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:15:46.081][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:15:46.082][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.084][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.085][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.086][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.087][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.088][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.089][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.091][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.093][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.094][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.096][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.098][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.099][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.100][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.101][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.102][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:15:46.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.109][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.114][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.115][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.116][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.117][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.119][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-03 19:15:46.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:46.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:46.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:46.129][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:46.130][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:46.131][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:46.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:15:46.135][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.137][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.138][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.151][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.152][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.153][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.156][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.158][private$selectFields]
biodb.TRACE[2024-03-03 19:15:46.159][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:15:46.160][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:15:46.161][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.162][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.163][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.164][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.165][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.166][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.167][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.168][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.169][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.170][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.171][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:15:46.172][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.173][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.174][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.175][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.176][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:15:46.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.184][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.185][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.186][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.188][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.189][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:15:46.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.229][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-03 19:15:46.230][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-03 19:15:46.231][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-03 19:15:46.242][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-03 19:15:46.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-03 19:15:46.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-03 19:15:46.253][biodb::testThat]
biodb.INFO [2024-03-03 19:15:46.254][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2024-03-03 19:15:46.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:15:46.256][biodb::testThat]
biodb.TRACE[2024-03-03 19:15:46.276][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2024-03-03 19:15:46.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2024-03-03 19:15:46.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.281][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:46.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2024-03-03 19:15:46.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.286][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.296][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.299][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.301][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:15:46.306][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:15:46.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:15:46.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:15:46.317][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:15:46.318][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:15:46.320][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:15:46.326][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:15:46.328][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:15:46.329][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:15:46.330][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:15:46.335][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2024-03-03 19:15:46.339][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:15:46.340][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:15:46.342][private$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[2024-03-03 19:15:50.307][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[2024-03-03 19:16:01.714][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:16:01.717][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2024-03-03 19:16:01.824][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2024-03-03 19:16:02.945][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-03 19:16:02.947][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:02.948][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:02.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:02.959][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:02.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:02.962][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:02.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:16:02.965][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:02.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:02.969][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:02.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:02.976][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:02.977][private$selectFields]
biodb.TRACE[2024-03-03 19:16:02.978][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:16:02.979][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:16:02.981][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:02.982][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.983][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.984][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:02.985][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:02.986][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.989][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.990][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:02.991][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:02.993][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:02.994][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:02.995][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.996][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:02.997][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:02.999][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.000][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:16:03.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.006][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.012][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.015][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.016][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.018][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2024-03-03 19:16:03.019][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:03.019][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:03.020][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:03.029][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:03.030][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:03.031][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:03.032][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:16:03.033][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.037][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.040][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.041][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.042][private$selectFields]
biodb.TRACE[2024-03-03 19:16:03.043][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:16:03.044][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:16:03.045][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.046][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.046][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.047][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.048][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.049][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.050][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.051][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.051][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.052][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.053][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.054][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.055][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.056][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.056][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.057][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:16:03.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.061][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.062][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.063][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.064][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.065][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.066][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.068][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2024-03-03 19:16:03.069][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:03.070][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:03.071][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:03.078][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:03.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:03.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:03.082][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.TRACE[2024-03-03 19:16:03.084][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.095][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.096][private$selectFields]
biodb.TRACE[2024-03-03 19:16:03.097][private$selectFields] Fields is null: FALSE
biodb.TRACE[2024-03-03 19:16:03.098][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:16:03.099][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.101][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.102][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.103][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.105][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.106][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.108][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.109][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.110][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.111][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.112][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:16:03.113][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.114][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.115][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.116][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.117][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2024-03-03 19:16:03.118][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.174][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:03.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:03.179][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2024-03-03 19:16:03.180][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2024-03-03 19:16:03.182][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2024-03-03 19:16:03.224][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2024-03-03 19:16:03.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2024-03-03 19:16:03.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:03.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2024-03-03 19:16:03.235][biodb::testThat]
biodb.INFO [2024-03-03 19:16:03.237][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2024-03-03 19:16:03.238][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:16:03.239][biodb::testThat]
biodb.DEBUG[2024-03-03 19:16:03.240][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2024-03-03 19:16:03.241][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2024-03-03 19:16:03.243][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2024-03-03 19:16:03.244][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2024-03-03 19:16:03.246][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-03 19:16:03.247][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-03 19:16:03.248][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:16:03.250][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-03 19:16:03.251][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-03 19:16:03.264][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:03.265][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:03.266][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:03.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:03.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:03.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:03.277][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:03.279][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2024-03-03 19:16:03.284][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:03.285][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:03.287][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:03.909][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:03.954][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:03.956][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[2024-03-03 19:16:03.958][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:04.580][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:04.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:04.583][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:04.585][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:05.233][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:05.236][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:05.238][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[2024-03-03 19:16:05.239][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:05.804][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:05.806][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:05.807][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:05.809][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:06.410][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:06.412][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:06.413][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[2024-03-03 19:16:06.414][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:07.033][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:07.035][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:07.037][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:07.038][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:07.663][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:07.665][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:07.667][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[2024-03-03 19:16:07.669][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:08.270][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:08.272][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:08.274][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:08.276][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:08.900][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:08.902][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:08.903][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[2024-03-03 19:16:08.904][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:09.563][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:09.576][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:09.577][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:09.579][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:10.204][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:10.206][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:10.208][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[2024-03-03 19:16:10.209][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:10.826][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:10.831][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:10.833][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:10.835][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:11.459][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:11.460][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:11.461][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[2024-03-03 19:16:11.461][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:12.080][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:12.094][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:12.095][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:12.097][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:12.740][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:12.742][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:12.743][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[2024-03-03 19:16:12.744][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:13.554][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:13.556][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:13.558][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:13.559][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:14.138][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:14.139][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:14.140][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[2024-03-03 19:16:14.142][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:14.783][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:14.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:14.786][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:14.788][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2024-03-03 19:16:15.374][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:15.376][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:15.377][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[2024-03-03 19:16:15.379][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2024-03-03 19:16:15.958][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-03 19:16:15.961][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2024-03-03 19:16:15.964][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-03 19:16:15.966][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2024-03-03 19:16:15.968][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-03 19:16:15.969][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:15.970][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:15.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:15.980][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:15.982][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:15.983][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:15.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:16:15.987][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:15.989][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:15.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:15.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:15.994][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:15.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:15.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:15.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:16.000][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:16.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:16.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:16.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:16.006][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:16.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:16.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:16.010][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:16.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:16.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:16.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:16.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:16.017][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:16.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:16.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:16.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:16.020][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:16.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:16.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:16.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:16.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:16.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:16.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:16.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:16:16.031][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2024-03-03 19:16:16.032][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2024-03-03 19:16:16.047][biodb::testThat]
biodb.INFO [2024-03-03 19:16:16.048][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2024-03-03 19:16:16.050][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:16:16.051][biodb::testThat]
biodb.DEBUG[2024-03-03 19:16:16.101][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2024-03-03 19:16:16.103][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2024-03-03 19:16:16.105][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-03 19:16:16.107][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2024-03-03 19:16:16.108][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2024-03-03 19:16:16.110][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2024-03-03 19:16:16.111][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-03 19:16:16.112][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:16:16.114][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-03 19:16:16.115][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-03 19:16:16.120][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:16.121][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:16.122][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:16.130][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:16.131][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:16.132][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:16.133][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:16.135][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2024-03-03 19:16:16.140][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:16.141][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:16.143][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:16.722][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:16.723][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:16.725][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:16.726][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:17.315][private$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[2024-03-03 19:16:17.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:17.319][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:17.320][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:17.904][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:17.906][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:17.908][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:17.910][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:19.193][private$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[2024-03-03 19:16:19.195][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:19.196][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:19.198][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:19.783][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:19.785][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:19.787][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:19.788][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:20.739][private$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[2024-03-03 19:16:20.741][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:20.742][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:20.744][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:21.328][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:21.330][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:21.331][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:21.333][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:21.927][private$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[2024-03-03 19:16:21.929][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:21.931][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:21.933][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:22.514][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:22.516][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:22.517][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:22.519][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:23.098][private$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[2024-03-03 19:16:23.100][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:23.101][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:23.104][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:23.668][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:23.670][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:23.671][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:23.672][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:24.246][private$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[2024-03-03 19:16:24.248][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:24.250][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:24.251][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:24.828][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:24.829][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:24.830][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:24.831][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:25.512][private$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[2024-03-03 19:16:25.514][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:25.516][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:25.517][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:26.101][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:26.103][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:26.104][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:26.106][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:26.685][private$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[2024-03-03 19:16:26.687][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:26.689][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:26.691][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:27.273][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:27.274][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:27.276][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:27.278][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:27.855][private$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[2024-03-03 19:16:27.857][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:27.858][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:27.860][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2024-03-03 19:16:28.450][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:28.451][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:28.453][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:16:28.454][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2024-03-03 19:16:29.030][private$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[2024-03-03 19:16:29.031][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:29.033][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:29.034][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:29.043][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:29.045][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:29.046][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:29.047][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:29.049][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2024-03-03 19:16:29.053][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:29.054][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:29.056][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:29.639][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:29.641][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:29.642][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[2024-03-03 19:16:29.643][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:30.238][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:30.240][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:30.241][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:30.243][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:30.829][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:30.830][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:30.831][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[2024-03-03 19:16:30.833][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:31.399][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:31.401][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:31.402][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:31.403][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:31.992][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:31.993][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:31.995][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[2024-03-03 19:16:31.997][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:32.566][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:32.567][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:32.569][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:32.615][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:33.195][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:33.197][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:33.198][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[2024-03-03 19:16:33.199][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:33.829][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:33.831][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:33.832][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:33.834][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:34.408][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:34.409][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:34.410][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[2024-03-03 19:16:34.412][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:34.980][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:34.981][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:34.982][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:34.984][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:35.562][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:35.564][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:35.565][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[2024-03-03 19:16:35.566][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:36.569][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:36.571][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:36.572][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:36.573][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:37.152][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:37.153][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:37.155][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[2024-03-03 19:16:37.156][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:37.714][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:37.715][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:37.717][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:37.719][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:38.296][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:38.298][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:38.299][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[2024-03-03 19:16:38.303][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:38.877][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:38.879][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:38.880][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:38.882][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:39.455][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:39.457][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:39.458][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[2024-03-03 19:16:39.460][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:40.130][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:16:40.131][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:40.133][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:40.135][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2024-03-03 19:16:40.706][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:16:40.708][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:16:40.710][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[2024-03-03 19:16:40.711][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.INFO [2024-03-03 19:16:41.292][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-03 19:16:41.295][private$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[2024-03-03 19:16:41.297][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-03 19:16:41.299][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-03 19:16:41.300][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-03 19:16:41.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:41.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:41.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:41.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:41.312][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:41.313][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:41.315][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:16:41.317][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.319][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.321][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.322][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.323][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.324][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.326][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.328][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:16:41.330][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:16:41.331][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:41.332][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:41.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:41.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:41.343][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:41.344][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:16:41.347][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.351][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:16:41.354][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.356][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.360][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.363][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.369][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.370][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.375][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.379][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.380][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.384][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.391][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:41.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:16:41.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:16:41.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:41.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:16:41.409][self$createEntryFromContent] Accession numbers: NA, NA.
biodb.DEBUG[2024-03-03 19:16:41.409][self$createEntryFromContent] Found 2 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-03 19:16:41.410][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, NULL"
biodb.INFO [2024-03-03 19:16:41.736][biodb::testThat]
biodb.INFO [2024-03-03 19:16:41.738][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2024-03-03 19:16:41.739][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:16:41.740][biodb::testThat]
biodb.INFO [2024-03-03 19:16:41.808][biodb::testThat]
biodb.INFO [2024-03-03 19:16:41.810][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2024-03-03 19:16:41.811][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:16:41.812][biodb::testThat]
biodb.INFO [2024-03-03 19:16:41.828][biodb::testThat]
biodb.INFO [2024-03-03 19:16:41.830][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2024-03-03 19:16:41.831][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:16:41.832][biodb::testThat]
biodb.DEBUG[2024-03-03 19:16:41.836][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2024-03-03 19:16:41.841][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:16:41.843][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:16:41.845][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2024-03-03 19:16:45.788][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2024-03-03 19:16:57.345][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:16:57.379][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2024-03-03 19:16:58.005][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2024-03-03 19:16:59.206][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:16:59.208][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:16:59.210][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:59.211][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:16:59.212][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:16:59.213][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:16:59.214][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:16:59.215][ef$get] fields variable is a list.
biodb.INFO [2024-03-03 19:16:59.217][biodb::testThat]
biodb.INFO [2024-03-03 19:16:59.218][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2024-03-03 19:16:59.219][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:16:59.220][biodb::testThat]
biodb.ERROR[2024-03-03 19:16:59.240][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2024-03-03 19:16:59.262][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2024-03-03 19:16:59.304][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-03 19:16:59.309][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-03 19:16:59.310][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-03 19:16:59.312][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-03 19:16:59.313][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.315][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.316][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.318][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.319][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.INFO [2024-03-03 19:16:59.333][biodb::testContext]
biodb.INFO [2024-03-03 19:16:59.335][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-03 19:16:59.336][biodb::testContext] Test context - Web services tests
biodb.INFO [2024-03-03 19:16:59.337][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-03 19:16:59.338][biodb::testContext]
biodb.INFO [2024-03-03 19:16:59.341][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-03 19:16:59.342][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-03 19:16:59.348][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:16:59.350][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-03 19:16:59.352][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-03 19:16:59.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.355][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.356][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-03 19:16:59.358][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-03 19:16:59.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.361][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[2024-03-03 19:16:59.362][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-03 19:16:59.363][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-03 19:16:59.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.365][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.366][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-03 19:16:59.368][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-03 19:16:59.369][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-03 19:16:59.370][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.373][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-03 19:16:59.374][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-03 19:16:59.375][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-03 19:16:59.375][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.377][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.378][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-03 19:16:59.379][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-03 19:16:59.379][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.380][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.381][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.382][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-03 19:16:59.382][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-03 19:16:59.383][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-03 19:16:59.384][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.386][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-03 19:16:59.387][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-03 19:16:59.388][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.390][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.391][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-03 19:16:59.391][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-03 19:16:59.392][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-03 19:16:59.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.395][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.395][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-03 19:16:59.396][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-03 19:16:59.397][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-03 19:16:59.398][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-03 19:16:59.399][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-03 19:16:59.400][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-03 19:16:59.401][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.402][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.403][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-03 19:16:59.404][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-03 19:16:59.406][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.407][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.408][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.409][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-03 19:16:59.410][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-03 19:16:59.411][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.412][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.413][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.415][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-03 19:16:59.448][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-03 19:16:59.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.454][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-03 19:16:59.455][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-03 19:16:59.457][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.458][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.459][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.461][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-03 19:16:59.462][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-03 19:16:59.463][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.465][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.466][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.467][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-03 19:16:59.469][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-03 19:16:59.512][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-03 19:16:59.514][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.516][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.517][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.519][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-03 19:16:59.520][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-03 19:16:59.522][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-03 19:16:59.523][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.524][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.526][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.527][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-03 19:16:59.529][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.531][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-03 19:16:59.532][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.534][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:16:59.535][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.536][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.538][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.539][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.540][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:16:59.542][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:16:59.543][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.544][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-03 19:16:59.545][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:16:59.547][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.548][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.551][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:16:59.551][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:16:59.551][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-03 19:16:59.551][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-03 19:16:59.551][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-03 19:16:59.553][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:16:59.557][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.561][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.568][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:16:59.574][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.576][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.578][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.581][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.584][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:16:59.585][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:16:59.588][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.590][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.592][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-03 19:16:59.597][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.599][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-03 19:16:59.602][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.604][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:16:59.605][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.606][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.607][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.608][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.609][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-03 19:16:59.610][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:16:59.611][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.613][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-03 19:16:59.614][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:16:59.615][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.616][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.617][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:16:59.617][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:16:59.617][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-03 19:16:59.617][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-03 19:16:59.617][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-03 19:16:59.618][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:16:59.619][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.621][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.622][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:16:59.623][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.624][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.625][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.627][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.628][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:16:59.629][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:16:59.631][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.632][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.633][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-03 19:16:59.636][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.637][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-03 19:16:59.638][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.640][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:16:59.641][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.642][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.643][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.644][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.646][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:16:59.647][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:16:59.649][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.650][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-03 19:16:59.651][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:16:59.653][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.654][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.655][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.656][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:16:59.657][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.657][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.658][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:16:59.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.662][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.663][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.664][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:16:59.665][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:16:59.666][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.667][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.668][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-03 19:16:59.670][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.671][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-03 19:16:59.672][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.674][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:16:59.675][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.675][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.676][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.678][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.678][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-03 19:16:59.679][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:16:59.680][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.681][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-03 19:16:59.682][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:16:59.683][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.684][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:16:59.685][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.685][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:16:59.686][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.687][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.688][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:16:59.689][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:16:59.690][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:16:59.691][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:16:59.691][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.692][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:16:59.693][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:16:59.694][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:16:59.694][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:16:59.696][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:16:59.696][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.697][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.698][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.705][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.706][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.707][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.710][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.712][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.731][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[2024-03-03 19:16:59.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.734][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.737][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.740][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.742][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[2024-03-03 19:16:59.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.743][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.744][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.746][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.747][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.748][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.752][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.753][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.754][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.756][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.758][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[2024-03-03 19:16:59.759][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.765][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[2024-03-03 19:16:59.766][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.766][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.767][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.770][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.775][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.776][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.778][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.778][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.780][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.781][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.782][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.783][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.784][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.785][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.786][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.787][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.788][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.791][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.795][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.796][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-03 19:16:59.798][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-03 19:16:59.812][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-03 19:16:59.813][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-03 19:16:59.815][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-03 19:16:59.816][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-03 19:16:59.817][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-03 19:16:59.818][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-03 19:16:59.819][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-03 19:16:59.821][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-03 19:16:59.823][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-03 19:16:59.824][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-03 19:16:59.826][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-03 19:16:59.828][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-03 19:16:59.829][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-03 19:16:59.831][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-03 19:16:59.833][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-03 19:16:59.835][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-03 19:16:59.837][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-03 19:16:59.838][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-03 19:16:59.839][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-03 19:16:59.840][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-03 19:16:59.842][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-03 19:16:59.843][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-03 19:16:59.844][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-03 19:16:59.845][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-03 19:16:59.847][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-03 19:16:59.849][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-03 19:16:59.850][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-03 19:16:59.851][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-03 19:16:59.853][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-03 19:16:59.854][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-03 19:16:59.856][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-03 19:16:59.858][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-03 19:16:59.859][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-03 19:16:59.860][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-03 19:16:59.862][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-03 19:16:59.863][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-03 19:16:59.864][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-03 19:16:59.865][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-03 19:16:59.866][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-03 19:16:59.867][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-03 19:16:59.869][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-03 19:16:59.871][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-03 19:16:59.872][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-03 19:16:59.873][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-03 19:16:59.875][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-03 19:16:59.876][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-03 19:16:59.878][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-03 19:16:59.879][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-03 19:16:59.880][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-03 19:16:59.881][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-03 19:16:59.883][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-03 19:16:59.884][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-03 19:16:59.886][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-03 19:16:59.888][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-03 19:16:59.889][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-03 19:16:59.891][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-03 19:16:59.893][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-03 19:16:59.895][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-03 19:16:59.897][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-03 19:16:59.898][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-03 19:16:59.899][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-03 19:16:59.900][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-03 19:16:59.901][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-03 19:16:59.903][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-03 19:16:59.904][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-03 19:16:59.905][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-03 19:16:59.906][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-03 19:16:59.908][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-03 19:16:59.909][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-03 19:16:59.910][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-03 19:16:59.912][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-03 19:16:59.913][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-03 19:16:59.914][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-03 19:16:59.916][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-03 19:16:59.918][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-03 19:16:59.920][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-03 19:16:59.922][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-03 19:16:59.924][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-03 19:16:59.925][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-03 19:16:59.926][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-03 19:16:59.927][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-03 19:16:59.928][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-03 19:16:59.930][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-03 19:16:59.931][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:16:59.931][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.933][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.934][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.936][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.939][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.942][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.950][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.950][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.951][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.952][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.954][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.959][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.960][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.961][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.964][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.971][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.972][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.973][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.974][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.984][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.986][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.987][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.988][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.990][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:16:59.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:16:59.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:16:59.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:16:59.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:16:59.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:16:59.997][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:16:59.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.005][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.007][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.009][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.010][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.012][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.013][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.015][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.016][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.017][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.018][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.023][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.025][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.026][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.027][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.028][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.029][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.031][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.032][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.033][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.034][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.039][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:00.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:00.054][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:00.055][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:00.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:00.057][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:00.057][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:00.058][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[2024-03-03 19:17:00.060][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-03 19:17:00.061][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:17:00.063][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:00.064][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-03 19:17:00.064][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:00.065][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:17:00.066][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:00.067][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:17:00.068][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:00.069][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:17:00.069][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:17:00.070][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:17:00.071][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:00.072][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-03 19:17:00.073][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-03 19:17:00.074][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:00.075][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:17:00.075][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:17:00.076][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:17:00.077][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:00.078][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:00.079][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:17:00.079][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:00.080][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:00.081][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:17:00.083][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:17:00.083][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-03 19:17:00.083][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:17:00.084][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:17:00.085][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:00.086][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:00.088][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-03 19:17:00.090][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-03 19:17:00.094][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:17:00.096][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-03 19:17:00.097][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:17:00.099][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-03 19:17:00.100][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-03 19:17:00.101][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-03 19:17:00.102][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-03 19:17:00.104][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-03 19:17:00.106][biodb::testThat]
biodb.INFO [2024-03-03 19:17:00.106][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2024-03-03 19:17:00.107][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:17:00.108][biodb::testThat]
biodb.DEBUG[2024-03-03 19:17:00.111][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[2024-03-03 19:17:00.115][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:00.115][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:00.117][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2024-03-03 19:17:00.760][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2024-03-03 19:17:01.397][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:17:01.400][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2024-03-03 19:17:01.406][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2024-03-03 19:17:01.422][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2024-03-03 19:17:01.442][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:01.444][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:01.447][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2024-03-03 19:17:02.099][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[2024-03-03 19:17:02.741][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:17:02.744][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2024-03-03 19:17:03.139][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2024-03-03 19:17:03.220][biodb::testThat]
biodb.INFO [2024-03-03 19:17:03.222][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2024-03-03 19:17:03.222][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:17:03.223][biodb::testThat]
biodb.INFO [2024-03-03 19:17:03.257][biodb::testThat]
biodb.INFO [2024-03-03 19:17:03.258][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2024-03-03 19:17:03.259][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:17:03.260][biodb::testThat]
biodb.DEBUG[2024-03-03 19:17:03.264][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[2024-03-03 19:17:03.267][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:03.268][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:03.269][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2024-03-03 19:17:03.754][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2024-03-03 19:17:04.236][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:17:04.238][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2024-03-03 19:17:04.304][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2024-03-03 19:17:04.309][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2024-03-03 19:17:04.338][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:17:04.340][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2024-03-03 19:17:04.341][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:17:04.344][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2024-03-03 19:17:04.350][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2024-03-03 19:17:04.356][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:04.358][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:04.361][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2024-03-03 19:17:04.845][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[2024-03-03 19:17:05.328][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:17:05.365][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2024-03-03 19:17:05.371][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2024-03-03 19:17:05.380][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[2024-03-03 19:17:05.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:05.385][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:05.387][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2024-03-03 19:17:06.715][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2024-03-03 19:17:09.883][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:17:09.915][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2024-03-03 19:17:09.979][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2024-03-03 19:17:10.125][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2024-03-03 19:17:10.128][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:10.129][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:10.131][private$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[2024-03-03 19:17:11.349][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[2024-03-03 19:17:14.923][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2024-03-03 19:17:14.925][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2024-03-03 19:17:14.940][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2024-03-03 19:17:15.135][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-03 19:17:15.137][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-03 19:17:15.139][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-03 19:17:15.140][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-03 19:17:15.141][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.144][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.147][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2024-03-03 19:17:15.152][biodb::testContext]
biodb.INFO [2024-03-03 19:17:15.153][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-03 19:17:15.153][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2024-03-03 19:17:15.154][biodb::testContext] ********************************************************************************
biodb.INFO [2024-03-03 19:17:15.155][biodb::testContext]
biodb.INFO [2024-03-03 19:17:15.157][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.10.0.
biodb.DEBUG[2024-03-03 19:17:15.158][self$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodb/definitions.yml".
biodb.DEBUG[2024-03-03 19:17:15.162][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:17:15.163][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2024-03-03 19:17:15.164][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2024-03-03 19:17:15.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.166][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.167][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2024-03-03 19:17:15.168][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2024-03-03 19:17:15.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.170][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.171][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2024-03-03 19:17:15.173][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2024-03-03 19:17:15.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.176][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.178][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2024-03-03 19:17:15.179][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2024-03-03 19:17:15.181][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2024-03-03 19:17:15.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.184][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.185][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2024-03-03 19:17:15.187][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2024-03-03 19:17:15.187][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2024-03-03 19:17:15.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.190][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.192][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2024-03-03 19:17:15.193][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2024-03-03 19:17:15.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.230][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.231][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2024-03-03 19:17:15.233][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2024-03-03 19:17:15.234][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2024-03-03 19:17:15.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.237][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.238][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2024-03-03 19:17:15.240][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2024-03-03 19:17:15.241][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.244][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2024-03-03 19:17:15.245][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2024-03-03 19:17:15.246][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2024-03-03 19:17:15.247][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.249][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2024-03-03 19:17:15.250][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2024-03-03 19:17:15.251][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2024-03-03 19:17:15.253][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2024-03-03 19:17:15.254][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2024-03-03 19:17:15.255][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2024-03-03 19:17:15.257][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.260][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2024-03-03 19:17:15.261][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2024-03-03 19:17:15.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.266][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2024-03-03 19:17:15.293][self$set] Set key entries.sep to "|".
biodb.DEBUG[2024-03-03 19:17:15.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.344][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[2024-03-03 19:17:15.346][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2024-03-03 19:17:15.350][self$set] Set key offline to FALSE.
biodb.DEBUG[2024-03-03 19:17:15.351][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.354][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.355][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2024-03-03 19:17:15.357][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2024-03-03 19:17:15.359][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.361][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[2024-03-03 19:17:15.362][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2024-03-03 19:17:15.363][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2024-03-03 19:17:15.364][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.368][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2024-03-03 19:17:15.369][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2024-03-03 19:17:15.393][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2024-03-03 19:17:15.404][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.410][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.411][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.412][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2024-03-03 19:17:15.413][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2024-03-03 19:17:15.414][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2024-03-03 19:17:15.415][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.418][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.419][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2024-03-03 19:17:15.421][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.422][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2024-03-03 19:17:15.423][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.425][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:17:15.426][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.427][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.428][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.429][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.430][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:17:15.431][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:17:15.434][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.435][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2024-03-03 19:17:15.435][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:17:15.437][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.438][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.439][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:17:15.439][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:17:15.439][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-03 19:17:15.439][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-03 19:17:15.439][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-03 19:17:15.441][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:17:15.442][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.443][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.444][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:17:15.446][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.447][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.447][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.448][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.449][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:17:15.450][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:17:15.451][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.451][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.453][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2024-03-03 19:17:15.455][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.457][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2024-03-03 19:17:15.458][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.459][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:17:15.460][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.461][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.462][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.464][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.465][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-03 19:17:15.467][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:17:15.468][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.469][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2024-03-03 19:17:15.470][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:17:15.471][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.472][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.473][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:17:15.473][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:17:15.473][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2024-03-03 19:17:15.473][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2024-03-03 19:17:15.473][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2024-03-03 19:17:15.474][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:17:15.475][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.475][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.476][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:17:15.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.479][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.480][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.482][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.483][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:17:15.484][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:17:15.485][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.486][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.487][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2024-03-03 19:17:15.489][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.490][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2024-03-03 19:17:15.491][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.493][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:17:15.494][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.496][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.498][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.499][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.501][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:17:15.507][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:17:15.508][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.511][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2024-03-03 19:17:15.515][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:17:15.516][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.518][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.519][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.520][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:17:15.521][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.522][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.523][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:17:15.524][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.526][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.527][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.529][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.530][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:17:15.531][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:17:15.532][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.533][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.534][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2024-03-03 19:17:15.536][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.537][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2024-03-03 19:17:15.538][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.539][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:17:15.540][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.541][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.542][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.566][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.568][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2024-03-03 19:17:15.570][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:17:15.572][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.573][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2024-03-03 19:17:15.575][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:17:15.577][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.579][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:15.580][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.581][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:17:15.582][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.583][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.584][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:17:15.585][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:15.586][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:15.587][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:17:15.588][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.589][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:17:15.590][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:17:15.591][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:15.592][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:15.594][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:17:15.596][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.597][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.598][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.599][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.600][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.602][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[2024-03-03 19:17:15.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.605][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.606][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.607][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.608][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.612][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.614][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.614][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.615][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.617][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.618][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.619][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.620][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.622][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.624][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.625][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.627][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.629][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.632][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.633][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.635][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.636][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.637][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.638][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.639][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.641][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.643][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.646][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.647][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.649][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.650][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.651][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.652][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.653][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.655][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.657][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.659][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.660][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.661][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.662][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.664][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.666][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.667][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.668][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.672][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.673][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.678][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.684][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.686][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.692][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.693][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2024-03-03 19:17:15.695][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2024-03-03 19:17:15.697][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2024-03-03 19:17:15.699][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2024-03-03 19:17:15.701][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2024-03-03 19:17:15.703][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2024-03-03 19:17:15.705][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2024-03-03 19:17:15.707][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2024-03-03 19:17:15.709][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2024-03-03 19:17:15.711][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2024-03-03 19:17:15.712][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2024-03-03 19:17:15.714][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2024-03-03 19:17:15.716][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2024-03-03 19:17:15.718][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2024-03-03 19:17:15.720][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2024-03-03 19:17:15.722][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-03 19:17:15.724][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2024-03-03 19:17:15.726][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2024-03-03 19:17:15.728][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2024-03-03 19:17:15.730][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2024-03-03 19:17:15.732][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2024-03-03 19:17:15.734][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2024-03-03 19:17:15.736][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2024-03-03 19:17:15.738][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2024-03-03 19:17:15.739][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2024-03-03 19:17:15.740][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2024-03-03 19:17:15.742][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2024-03-03 19:17:15.744][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2024-03-03 19:17:15.745][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2024-03-03 19:17:15.747][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2024-03-03 19:17:15.749][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2024-03-03 19:17:15.751][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2024-03-03 19:17:15.753][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2024-03-03 19:17:15.755][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2024-03-03 19:17:15.757][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2024-03-03 19:17:15.758][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2024-03-03 19:17:15.760][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2024-03-03 19:17:15.762][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2024-03-03 19:17:15.764][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2024-03-03 19:17:15.766][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2024-03-03 19:17:15.767][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2024-03-03 19:17:15.768][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2024-03-03 19:17:15.769][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2024-03-03 19:17:15.770][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2024-03-03 19:17:15.772][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2024-03-03 19:17:15.773][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2024-03-03 19:17:15.774][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2024-03-03 19:17:15.776][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2024-03-03 19:17:15.778][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2024-03-03 19:17:15.780][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2024-03-03 19:17:15.782][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2024-03-03 19:17:15.784][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2024-03-03 19:17:15.786][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2024-03-03 19:17:15.787][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2024-03-03 19:17:15.788][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2024-03-03 19:17:15.790][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2024-03-03 19:17:15.792][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2024-03-03 19:17:15.794][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2024-03-03 19:17:15.796][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2024-03-03 19:17:15.798][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2024-03-03 19:17:15.800][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2024-03-03 19:17:15.802][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2024-03-03 19:17:15.803][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2024-03-03 19:17:15.805][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2024-03-03 19:17:15.807][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2024-03-03 19:17:15.809][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2024-03-03 19:17:15.811][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2024-03-03 19:17:15.812][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2024-03-03 19:17:15.813][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2024-03-03 19:17:15.815][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2024-03-03 19:17:15.817][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2024-03-03 19:17:15.819][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2024-03-03 19:17:15.821][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2024-03-03 19:17:15.823][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2024-03-03 19:17:15.825][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2024-03-03 19:17:15.826][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2024-03-03 19:17:15.828][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2024-03-03 19:17:15.829][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2024-03-03 19:17:15.831][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2024-03-03 19:17:15.833][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2024-03-03 19:17:15.834][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2024-03-03 19:17:15.836][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2024-03-03 19:17:15.837][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2024-03-03 19:17:15.856][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2024-03-03 19:17:15.859][initialize] This is biodb version 1.10.0.
biodb.DEBUG[2024-03-03 19:17:15.860][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2024-03-03 19:17:15.862][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.863][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.864][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.865][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.867][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.868][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.869][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.870][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.874][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.877][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.880][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.881][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.881][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.882][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.884][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.885][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.886][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.887][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.889][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.890][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.892][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.897][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[2024-03-03 19:17:15.897][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.898][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.899][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.903][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[2024-03-03 19:17:15.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.907][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.910][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.911][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[2024-03-03 19:17:15.912][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.917][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.919][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.920][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.922][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.923][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.941][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.945][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.947][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.948][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.949][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.950][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.954][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.955][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.956][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.957][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.958][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.960][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.961][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.963][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.963][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.967][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.967][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.969][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.970][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.972][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.978][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.981][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.982][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.983][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.989][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.990][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.992][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.992][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:15.995][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:15.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:15.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:15.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:15.998][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:15.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2024-03-03 19:17:15.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:16.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:16.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:16.003][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:16.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:16.006][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2024-03-03 19:17:16.007][biodb$loadDefinitions] Load definitions from file "/Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2024-03-03 19:17:16.009][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:17:16.010][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:16.011][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2024-03-03 19:17:16.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:16.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2024-03-03 19:17:16.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:16.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2024-03-03 19:17:16.017][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:16.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2024-03-03 19:17:16.020][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2024-03-03 19:17:16.021][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2024-03-03 19:17:16.022][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:16.023][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2024-03-03 19:17:16.024][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2024-03-03 19:17:16.025][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2024-03-03 19:17:16.026][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2024-03-03 19:17:16.027][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2024-03-03 19:17:16.027][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2024-03-03 19:17:16.028][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2024-03-03 19:17:16.029][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:16.029][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:16.030][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2024-03-03 19:17:16.031][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2024-03-03 19:17:16.032][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2024-03-03 19:17:16.033][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2024-03-03 19:17:16.034][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:17:16.034][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2024-03-03 19:17:16.035][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2024-03-03 19:17:16.036][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2024-03-03 19:17:16.037][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2024-03-03 19:17:16.038][self$setPropertyValue]
biodb.DEBUG[2024-03-03 19:17:16.039][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2024-03-03 19:17:16.040][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2024-03-03 19:17:16.043][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:17:16.045][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2024-03-03 19:17:16.046][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2024-03-03 19:17:16.047][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2024-03-03 19:17:16.049][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-03 19:17:16.050][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2024-03-03 19:17:16.052][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2024-03-03 19:17:16.054][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2024-03-03 19:17:16.055][biodb::testThat]
biodb.INFO [2024-03-03 19:17:16.057][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2024-03-03 19:17:16.058][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2024-03-03 19:17:16.060][biodb::testThat]
biodb.DEBUG[2024-03-03 19:17:16.065][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[2024-03-03 19:17:16.070][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2024-03-03 19:17:16.072][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2024-03-03 19:17:16.074][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2024-03-03 19:17:16.125][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2024-03-03 19:17:17.522][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2024-03-03 19:17:17.523][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2024-03-03 19:17:17.525][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2024-03-03 19:17:17.527][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2024-03-03 19:17:17.529][loadFileContents] Loaded 1 files from cache: [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2024-03-03 19:17:17.530][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2024-03-03 19:17:17.532][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2024-03-03 19:17:17.533][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2024-03-03 19:17:17.534][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2024-03-03 19:17:17.538][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:17:17.539][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:17.540][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:17.549][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:17.551][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:17.552][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:17.553][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[2024-03-03 19:17:17.555][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2024-03-03 19:17:17.559][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:17.560][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:17.562][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:18.167][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:18.168][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:18.170][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:18.171][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:18.743][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:18.745][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:18.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:18.747][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:19.335][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:19.337][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:19.338][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:19.340][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:20.087][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:20.096][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:20.098][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:20.100][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:20.683][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:20.686][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:20.688][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:20.689][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:21.571][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:21.573][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:21.574][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:21.576][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:22.158][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:22.159][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:22.160][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:22.161][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:23.006][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:23.029][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:23.031][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:23.033][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:23.617][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:23.633][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:23.634][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:23.636][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:24.204][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:24.206][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:24.207][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:24.209][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:24.779][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:24.803][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:24.805][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:24.806][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:25.383][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:25.384][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:25.385][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:25.387][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:25.941][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:25.942][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:25.944][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:25.945][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:26.520][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:26.521][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:26.522][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:26.524][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:27.101][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:27.103][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:27.105][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:27.106][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:27.781][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:27.789][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:27.791][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:27.793][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:28.370][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:28.372][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:28.373][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:28.375][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:29.351][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.DEBUG[2024-03-03 19:17:29.352][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2024-03-03 19:17:29.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2024-03-03 19:17:29.355][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2024-03-03 19:17:29.935][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv does not exist.
biodb.TRACE[2024-03-03 19:17:29.954][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2024-03-03 19:17:29.956][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2024-03-03 19:17:29.958][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.INFO [2024-03-03 19:17:30.799][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv". Retrying connection to server...
biodb.TRACE[2024-03-03 19:17:30.802][private$doSaveContentToFile] Saving to cache [1]: "/Users/biocbuild/Library/Caches/org.R-project.R/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2024-03-03 19:17:30.804][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2024-03-03 19:17:30.805][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2024-03-03 19:17:30.807][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2024-03-03 19:17:30.808][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:17:30.809][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:30.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:30.839][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:30.840][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:30.841][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:30.842][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:17:30.845][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:30.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:30.848][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.849][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.851][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:30.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:30.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:30.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:30.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:17:30.860][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:17:30.861][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:30.861][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:30.873][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:30.875][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:30.897][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:30.899][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:17:30.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:30.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:30.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.913][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:30.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:30.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.918][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:30.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:30.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.923][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:30.924][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:30.925][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.928][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:17:30.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2024-03-03 19:17:30.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.933][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:17:30.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2024-03-03 19:17:30.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.938][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.939][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:30.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:30.942][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.945][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:30.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:30.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.949][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.969][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:30.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:30.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.976][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:30.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:30.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.982][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:17:30.984][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:30.985][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.986][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.988][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2024-03-03 19:17:30.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:30.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.993][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:30.994][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:30.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:30.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:30.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.000][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.007][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.008][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.009][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.013][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.019][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:17:31.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.067][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2024-03-03 19:17:31.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.072][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.076][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.081][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2024-03-03 19:17:31.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.086][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.091][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.094][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.095][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.096][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.099][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.126][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.131][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.133][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.134][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.135][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.136][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.138][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.139][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.140][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.141][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.142][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.143][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.145][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.146][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.147][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.148][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.149][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.151][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.157][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.159][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.160][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.161][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.162][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.172][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.177][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2024-03-03 19:17:31.201][self$createEntryFromContent] Accession numbers: NA, LMFA00000002.
biodb.DEBUG[2024-03-03 19:17:31.202][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2024-03-03 19:17:31.205][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2024-03-03 19:17:31.206][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:17:31.207][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:31.208][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:31.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:31.220][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:31.221][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:31.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:17:31.223][private$entriesToListOfDataframes] Entry converted to data frame: NULL.
biodb.DEBUG[2024-03-03 19:17:31.225][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2024-03-03 19:17:31.225][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:31.226][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:31.235][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:31.236][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:31.238][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:31.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2024-03-03 19:17:31.242][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:17:31.243][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:17:31.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.247][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2024-03-03 19:17:31.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2024-03-03 19:17:31.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.274][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2024-03-03 19:17:31.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2024-03-03 19:17:31.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.277][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2024-03-03 19:17:31.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2024-03-03 19:17:31.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.281][private$selectFields] Fields none
biodb.TRACE[2024-03-03 19:17:31.281][private$selectFields]
biodb.TRACE[2024-03-03 19:17:31.282][private$selectFields] Fields is null: TRUE
biodb.TRACE[2024-03-03 19:17:31.283][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2024-03-03 19:17:31.284][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:17:31.284][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.285][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.286][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.288][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.289][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.290][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.291][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.293][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.294][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.295][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.296][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.297][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.298][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.299][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.300][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.301][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.302][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.304][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.305][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.306][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.308][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.309][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.310][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.311][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.314][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.315][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.316][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.316][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.317][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.319][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.320][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.321][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.323][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.323][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.326][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.327][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.328][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.329][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.330][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.330][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.331][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.332][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.333][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.334][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.336][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.338][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.339][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.340][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.341][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.342][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.344][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.345][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.369][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.370][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.372][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.373][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.374][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.375][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.376][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.377][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.379][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:17:31.380][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2024-03-03 19:17:31.381][ef$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.382][ef$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.383][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.384][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.386][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.387][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.388][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.389][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.390][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.391][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.392][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.393][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.394][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.395][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.397][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.398][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.399][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.400][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.402][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.403][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.404][ef$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.405][ef$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.406][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.407][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.408][ef$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.409][ef$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.410][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.411][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.413][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.415][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.416][ef$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.417][ef$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.419][private$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[2024-03-03 19:17:31.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.450][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2024-03-03 19:17:31.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2024-03-03 19:17:31.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.462][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.463][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2024-03-03 19:17:31.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.476][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.478][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.479][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.480][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.482][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.483][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.484][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.487][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2024-03-03 19:17:31.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.492][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.497][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.498][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.501][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.507][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2024-03-03 19:17:31.510][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.519][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.520][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.526][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.528][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.529][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.531][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.532][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.533][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2024-03-03 19:17:31.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.537][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.542][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.548][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2024-03-03 19:17:31.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2024-03-03 19:17:31.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.554][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.558][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.561][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.563][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2024-03-03 19:17:31.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2024-03-03 19:17:31.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.569][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.571][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.574][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.575][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.579][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2024-03-03 19:17:31.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2024-03-03 19:17:31.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2024-03-03 19:17:31.608][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2024-03-03 19:17:31.611][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2024-03-03 19:17:31.612][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2024-03-03 19:17:31.621][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2024-03-03 19:17:31.622][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2024-03-03 19:17:31.623][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2024-03-03 19:17:31.624][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2024-03-03 19:17:31.625][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2024-03-03 19:17:31.625][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2024-03-03 19:17:31.626][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2024-03-03 19:17:31.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2024-03-03 19:17:31.628][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2024-03-03 19:17:31.629][FUN] Functions in observer 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 167 ]
══ 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 167 ]
Error: Test failures
Execution halted
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 2.416 | 0.960 | 3.446 | |
| LipidmapsStructureEntry | 0.504 | 0.023 | 0.543 | |