| Back to Build/check report for BioC 3.17: simplified long |
|
This page was generated on 2023-03-27 05:50:30 -0000 (Mon, 27 Mar 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) | aarch64 | R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences" | 6083 |
| 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 | ||||
|
To the developers/maintainers of the biodbLipidmaps package: - Please 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 How and When does the builder pull? When will my changes propagate? for more information. - Make sure to use the following settings in order to reproduce any error or warning you see on this page. |
| Package 197/2195 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.5.0 (landing page) Pierrick Roger
| kunpeng1 | Linux (Ubuntu 22.04.1 LTS) / aarch64 | OK | OK | OK | |||||||||
| Package: biodbLipidmaps |
| Version: 1.5.0 |
| Command: /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbLipidmaps_1.5.0.tar.gz |
| StartedAt: 2023-03-24 21:56:06 -0000 (Fri, 24 Mar 2023) |
| EndedAt: 2023-03-24 22:00:14 -0000 (Fri, 24 Mar 2023) |
| EllapsedTime: 248.3 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbLipidmaps_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2023-03-12 r83975)
* using platform: aarch64-unknown-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
GNU Fortran (Ubuntu 11.3.0-1ubuntu1~22.04) 11.3.0
* running under: Ubuntu 22.04.2 LTS
* using session charset: UTF-8
* checking for file ‘biodbLipidmaps/DESCRIPTION’ ... OK
* this is package ‘biodbLipidmaps’ version ‘1.5.0’
* 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
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
LipidmapsStructureConn 3.499 0.303 7.656
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ...
‘biodbLipidmaps.Rmd’ using ‘UTF-8’... OK
NONE
* checking re-building of vignette outputs ... OK
* checking PDF version of manual ... OK
* DONE
Status: OK
biodbLipidmaps.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD INSTALL biodbLipidmaps ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-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
R Under development (unstable) (2023-03-12 r83975) -- "Unsuffered Consequences"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-unknown-linux-gnu (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 [2023-03-24 21:56:57.354][biodb::testContext]
biodb.INFO [2023-03-24 21:56:57.357][biodb::testContext] ********************************************************************************
biodb.INFO [2023-03-24 21:56:57.358][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-03-24 21:56:57.360][biodb::testContext] ********************************************************************************
biodb.INFO [2023-03-24 21:56:57.361][biodb::testContext]
biodb.INFO [2023-03-24 21:56:57.381][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-03-24 21:56:57.384][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-03-24 21:56:57.393][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:56:57.395][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-03-24 21:56:57.397][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-03-24 21:56:57.398][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.399][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.402][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-03-24 21:56:57.429][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-03-24 21:56:57.430][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.432][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.433][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.434][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-03-24 21:56:57.436][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-03-24 21:56:57.437][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.441][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-03-24 21:56:57.443][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-03-24 21:56:57.444][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-03-24 21:56:57.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.448][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.450][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-03-24 21:56:57.451][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-03-24 21:56:57.453][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-03-24 21:56:57.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.458][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-03-24 21:56:57.460][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-03-24 21:56:57.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.464][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.465][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-03-24 21:56:57.466][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-03-24 21:56:57.468][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-03-24 21:56:57.469][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.470][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.472][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.473][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-03-24 21:56:57.475][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-03-24 21:56:57.476][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.477][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.479][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.480][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-03-24 21:56:57.482][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-03-24 21:56:57.483][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-03-24 21:56:57.484][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.487][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.488][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-03-24 21:56:57.490][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-03-24 21:56:57.491][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-03-24 21:56:57.493][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-03-24 21:56:57.494][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-03-24 21:56:57.496][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-03-24 21:56:57.497][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.498][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.501][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-03-24 21:56:57.503][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-03-24 21:56:57.504][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.507][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.508][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-03-24 21:56:57.510][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-03-24 21:56:57.511][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.512][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.514][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.515][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-03-24 21:56:57.517][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-03-24 21:56:57.518][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.519][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.521][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.522][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-03-24 21:56:57.523][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-03-24 21:56:57.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.529][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-03-24 21:56:57.530][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-03-24 21:56:57.532][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.533][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.536][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-03-24 21:56:57.537][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-03-24 21:56:57.541][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-03-24 21:56:57.543][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.545][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.547][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-03-24 21:56:57.548][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-03-24 21:56:57.550][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-03-24 21:56:57.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.554][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.559][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-03-24 21:56:57.606][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.638][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-03-24 21:56:57.639][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.641][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:56:57.642][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.643][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.645][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.646][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.647][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:56:57.649][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:56:57.650][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.651][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-03-24 21:56:57.653][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:56:57.654][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.655][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.657][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:56:57.657][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:56:57.657][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-03-24 21:56:57.657][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-03-24 21:56:57.657][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-03-24 21:56:57.658][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:56:57.659][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.661][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.662][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:56:57.663][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.664][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.666][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.667][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.668][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:56:57.669][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:56:57.671][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.672][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.674][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-03-24 21:56:57.676][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.677][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-03-24 21:56:57.679][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.680][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:56:57.681][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.683][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.684][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.685][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.687][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-03-24 21:56:57.688][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:56:57.689][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.691][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-03-24 21:56:57.692][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:56:57.693][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.695][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.696][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:56:57.696][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:56:57.696][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-03-24 21:56:57.696][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-03-24 21:56:57.696][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-03-24 21:56:57.697][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:56:57.699][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.700][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.701][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:56:57.702][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.704][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.705][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.706][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.707][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:56:57.709][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:56:57.710][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.711][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.713][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-03-24 21:56:57.715][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.716][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-03-24 21:56:57.718][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.719][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:56:57.720][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.722][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.723][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.724][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.726][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:56:57.727][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:56:57.728][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.730][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-03-24 21:56:57.731][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:56:57.732][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.734][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.735][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.736][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:56:57.738][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.739][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.740][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:56:57.741][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.743][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.744][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.745][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.747][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:56:57.748][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:56:57.749][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.750][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.752][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-03-24 21:56:57.754][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.756][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-03-24 21:56:57.757][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.758][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:56:57.760][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.761][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.762][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.764][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.765][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-03-24 21:56:57.766][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:56:57.768][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.769][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-03-24 21:56:57.770][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:56:57.772][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.773][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:57.774][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.776][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:56:57.777][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.778][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.779][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:56:57.781][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:57.782][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:57.783][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:56:57.785][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.786][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:56:57.787][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:56:57.788][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:57.790][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:57.795][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:56:57.796][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.797][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.798][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.801][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.803][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[2023-03-24 21:56:57.804][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.807][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.809][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[2023-03-24 21:56:57.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.813][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.814][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.815][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[2023-03-24 21:56:57.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.819][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.820][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.821][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[2023-03-24 21:56:57.822][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.823][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.825][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.826][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.827][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.828][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.829][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.830][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.833][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.834][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.836][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.840][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.842][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.843][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.847][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.848][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.849][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.851][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.852][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.854][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.855][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.856][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.858][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.861][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.862][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.864][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.865][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.866][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.867][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.868][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.869][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.871][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.872][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.873][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.874][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[2023-03-24 21:56:57.875][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.876][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.878][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.879][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.880][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.881][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.882][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.884][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.885][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.886][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.887][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.888][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.891][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:57.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:57.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:57.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:57.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:57.899][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-03-24 21:56:57.905][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-03-24 21:56:57.907][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-03-24 21:56:57.909][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-03-24 21:56:57.911][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-03-24 21:56:57.913][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-03-24 21:56:57.914][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-03-24 21:56:57.916][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-03-24 21:56:57.918][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-03-24 21:56:57.920][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-03-24 21:56:57.922][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-03-24 21:56:57.924][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-03-24 21:56:57.925][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-03-24 21:56:57.927][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-03-24 21:56:57.929][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-03-24 21:56:57.931][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-03-24 21:56:57.933][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-03-24 21:56:57.935][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-03-24 21:56:57.936][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-03-24 21:56:57.938][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-03-24 21:56:57.940][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-03-24 21:56:57.942][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-03-24 21:56:57.944][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-03-24 21:56:57.946][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-03-24 21:56:57.947][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-03-24 21:56:57.949][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-03-24 21:56:57.951][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-03-24 21:56:57.953][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-03-24 21:56:57.962][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-03-24 21:56:57.964][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-03-24 21:56:57.966][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-03-24 21:56:57.968][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-03-24 21:56:57.970][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-03-24 21:56:57.971][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-03-24 21:56:57.973][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-03-24 21:56:57.975][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-03-24 21:56:57.977][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-03-24 21:56:57.979][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-03-24 21:56:57.981][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-03-24 21:56:57.983][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-03-24 21:56:57.985][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-03-24 21:56:57.987][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-03-24 21:56:57.989][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-03-24 21:56:57.990][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-03-24 21:56:57.992][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-03-24 21:56:57.994][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-03-24 21:56:57.996][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-03-24 21:56:57.998][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-03-24 21:56:58.000][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-03-24 21:56:58.002][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-03-24 21:56:58.004][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-03-24 21:56:58.006][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-03-24 21:56:58.007][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-03-24 21:56:58.009][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-03-24 21:56:58.011][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-03-24 21:56:58.013][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-03-24 21:56:58.015][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-03-24 21:56:58.017][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-03-24 21:56:58.019][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-03-24 21:56:58.021][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-03-24 21:56:58.023][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-03-24 21:56:58.025][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-03-24 21:56:58.026][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-03-24 21:56:58.028][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-03-24 21:56:58.030][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-03-24 21:56:58.032][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-03-24 21:56:58.034][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-03-24 21:56:58.036][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-03-24 21:56:58.038][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-03-24 21:56:58.040][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-03-24 21:56:58.042][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-03-24 21:56:58.044][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-03-24 21:56:58.045][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-03-24 21:56:58.047][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-03-24 21:56:58.049][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-03-24 21:56:58.051][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-03-24 21:56:58.053][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-03-24 21:56:58.055][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-03-24 21:56:58.057][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-03-24 21:56:58.059][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-03-24 21:56:58.061][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-03-24 21:56:58.063][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-03-24 21:56:58.065][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-03-24 21:56:58.072][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-03-24 21:56:58.074][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-03-24 21:56:58.078][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:56:58.080][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.081][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.082][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.083][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.089][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.090][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.092][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.094][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.095][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.097][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.098][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.100][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.101][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.105][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.109][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.115][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.117][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.119][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.122][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[2023-03-24 21:56:58.123][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.124][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.127][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.128][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.130][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.131][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.134][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.135][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.136][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.137][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.139][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.142][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.145][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.146][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.147][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.148][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.149][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.151][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.153][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.154][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.155][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.157][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.158][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.159][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.165][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.166][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.168][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.169][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.170][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.171][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.172][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.174][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.175][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.176][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.178][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.180][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.181][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.187][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.188][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.189][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.190][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.193][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.195][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.198][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.199][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.201][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.204][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.206][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.207][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.216][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.217][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.218][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.221][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.224][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:56:58.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.227][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.229][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.230][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.231][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:56:58.234][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-03-24 21:56:58.246][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:56:58.248][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:58.249][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-03-24 21:56:58.251][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:58.252][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:56:58.253][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:58.255][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:56:58.256][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:58.257][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:56:58.259][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:56:58.260][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:56:58.261][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:58.263][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-03-24 21:56:58.264][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-03-24 21:56:58.265][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-03-24 21:56:58.267][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-03-24 21:56:58.268][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:56:58.268][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:56:58.270][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:56:58.271][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:58.272][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:58.274][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:56:58.275][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:56:58.276][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:56:58.277][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:56:58.279][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-03-24 21:56:58.279][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-03-24 21:56:58.280][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:56:58.281][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:56:58.282][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-03-24 21:56:58.284][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:56:58.299][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-03-24 21:56:58.301][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-03-24 21:56:58.330][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:56:58.331][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-03-24 21:56:58.337][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:56:58.342][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-03-24 21:56:58.348][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-03-24 21:56:58.349][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-03-24 21:56:58.351][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-03-24 21:56:58.352][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-03-24 21:56:58.372][biodb::testThat]
biodb.INFO [2023-03-24 21:56:58.373][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-03-24 21:56:58.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:56:58.376][biodb::testThat]
biodb.TRACE[2023-03-24 21:56:58.381][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-03-24 21:56:58.386][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-03-24 21:56:58.391][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-03-24 21:56:58.401][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:56:58.403][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:58.404][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:58.420][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:58.422][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:58.423][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:58.424][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:56:58.439][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.442][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.443][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.445][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.469][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:56:58.470][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:56:58.471][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.473][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.474][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:56:58.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:56:58.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.480][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:56:58.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:56:58.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.485][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:58.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:58.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.524][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:58.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:58.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.533][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:58.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:58.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.539][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:58.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:58.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.548][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:56:58.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:58.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.553][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:56:58.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:58.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.562][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:58.563][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:58.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.568][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:58.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:58.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.572][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.576][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.582][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.586][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.591][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:56:58.592][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.597][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:56:58.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.602][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.608][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.613][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:56:58.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.657][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.662][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.711][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.720][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.722][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.731][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.733][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.734][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.737][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.742][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.748][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.749][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.750][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.753][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.758][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.760][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.761][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.762][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.764][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.777][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.778][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.780][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.781][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.782][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.783][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.788][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:56:58.789][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-03-24 21:56:58.795][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:56:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:56:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:56:58.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:56:58.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-03-24 21:56:58.808][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-03-24 21:56:58.809][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.810][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.812][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-03-24 21:56:58.813][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-03-24 21:56:58.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.834][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.839][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.857][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.858][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.869][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.872][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.873][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.874][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.876][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.877][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.878][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.880][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.883][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.884][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.887][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.892][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.894][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.895][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.896][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.903][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.912][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.913][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.914][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:58.917][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.918][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.943][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.944][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.945][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.954][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.955][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.956][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.958][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.959][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:58.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:58.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.974][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.983][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.991][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.992][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.994][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:58.995][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:58.996][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:58.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:58.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.011][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.013][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.017][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.019][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.022][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.028][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.029][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.030][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.032][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.033][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.048][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.051][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.052][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.053][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.058][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.059][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.064][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.066][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.068][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.070][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.085][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.090][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.096][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.101][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.102][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.104][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.105][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.106][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.121][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.127][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.130][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.132][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.136][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.138][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.139][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.140][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.142][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.143][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.145][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.146][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.158][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.160][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.162][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.170][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.171][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.172][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.174][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.181][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.182][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.184][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.185][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.193][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.194][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.195][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.197][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.204][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.205][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.207][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.208][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.215][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.217][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.218][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.219][ef$get] fields variable is a list.
biodb.INFO [2023-03-24 21:56:59.261][biodb::testThat]
biodb.INFO [2023-03-24 21:56:59.262][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-03-24 21:56:59.264][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:56:59.265][biodb::testThat]
biodb.DEBUG[2023-03-24 21:56:59.283][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-03-24 21:56:59.293][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-03-24 21:56:59.298][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-03-24 21:56:59.300][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:56:59.301][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-03-24 21:56:59.303][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-03-24 21:56:59.362][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-03-24 21:56:59.363][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-03-24 21:56:59.366][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:56:59.367][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:56:59.368][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:56:59.375][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:56:59.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:56:59.378][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:56:59.379][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:56:59.385][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.393][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.394][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.399][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:56:59.400][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:56:59.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:56:59.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:56:59.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.413][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:56:59.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:56:59.416][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.417][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.419][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:56:59.420][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:56:59.421][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.424][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.430][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.431][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:56:59.432][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.438][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.440][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.441][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.442][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.444][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.445][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:56:59.446][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.448][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.452][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:56:59.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.458][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:56:59.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:56:59.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.466][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.472][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:56:59.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:56:59.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.481][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.485][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.486][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.489][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.490][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.495][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:56:59.496][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.500][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:56:59.502][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.506][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.510][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.511][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.516][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:56:59.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.520][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.525][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.530][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.532][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.533][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.544][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.550][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.551][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.553][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.554][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.555][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.564][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:59.566][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:59.567][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.568][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.570][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:59.571][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:59.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.575][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.578][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.579][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.580][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:59.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:56:59.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.589][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.597][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.598][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.599][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.606][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.610][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.611][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.612][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.614][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.615][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.616][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:56:59.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:56:59.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:56:59.622][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-03-24 21:56:59.623][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-03-24 21:56:59.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-03-24 21:56:59.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.629][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-03-24 21:56:59.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-03-24 21:56:59.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.634][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-03-24 21:56:59.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-03-24 21:56:59.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-03-24 21:56:59.647][biodb::testThat]
biodb.INFO [2023-03-24 21:56:59.648][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-03-24 21:56:59.649][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:56:59.651][biodb::testThat]
biodb.TRACE[2023-03-24 21:56:59.654][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.656][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.657][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.658][ef$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:56:59.660][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-03-24 21:56:59.696][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.702][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.706][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:56:59.707][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:56:59.709][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:56:59.710][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:56:59.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:56:59.715][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-03-24 21:56:59.731][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[2023-03-24 21:56:59.758][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:56:59.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:56:59.761][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-03-24 21:57:01.445][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-03-24 21:57:02.621][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:02.631][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-03-24 21:57:02.662][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-03-24 21:57:02.668][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-03-24 21:57:02.687][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:02.689][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:02.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:02.692][ef$get] fields variable is a list.
biodb.INFO [2023-03-24 21:57:02.694][biodb::testThat]
biodb.INFO [2023-03-24 21:57:02.696][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-03-24 21:57:02.697][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:02.698][biodb::testThat]
biodb.TRACE[2023-03-24 21:57:02.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:02.763][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:02.764][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:02.765][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:02.766][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:02.768][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:02.769][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:02.770][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:02.772][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:02.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:02.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:02.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:02.921][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-03-24 21:57:02.925][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-03-24 21:57:02.954][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-03-24 21:57:02.955][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:57:02.957][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-03-24 21:57:02.978][biodb::testThat]
biodb.INFO [2023-03-24 21:57:02.979][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-03-24 21:57:02.980][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:02.982][biodb::testThat]
biodb.TRACE[2023-03-24 21:57:03.015][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.020][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.023][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.024][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.025][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-03-24 21:57:03.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-03-24 21:57:03.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.030][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-03-24 21:57:03.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-03-24 21:57:03.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.092][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.093][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.095][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.096][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.097][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:57:03.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.102][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-03-24 21:57:03.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-03-24 21:57:03.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:03.107][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-03-24 21:57:03.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-03-24 21:57:03.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:03.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-03-24 21:57:03.116][biodb::testThat]
biodb.INFO [2023-03-24 21:57:03.117][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-03-24 21:57:03.118][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:03.119][biodb::testThat]
biodb.INFO [2023-03-24 21:57:03.125][biodb::testThat]
biodb.INFO [2023-03-24 21:57:03.127][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-03-24 21:57:03.128][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:03.129][biodb::testThat]
biodb.INFO [2023-03-24 21:57:03.135][biodb::testThat]
biodb.INFO [2023-03-24 21:57:03.136][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-03-24 21:57:03.137][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:03.138][biodb::testThat]
biodb.DEBUG[2023-03-24 21:57:03.142][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-03-24 21:57:04.495][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-03-24 21:57:05.328][biodb::testThat]
biodb.INFO [2023-03-24 21:57:05.329][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-03-24 21:57:05.331][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:05.332][biodb::testThat]
biodb.TRACE[2023-03-24 21:57:05.343][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:05.344][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:05.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.347][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.348][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.350][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.351][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.352][ef$get] fields variable is a list.
biodb.INFO [2023-03-24 21:57:05.354][biodb::testThat]
biodb.INFO [2023-03-24 21:57:05.356][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-03-24 21:57:05.357][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:05.358][biodb::testThat]
biodb.TRACE[2023-03-24 21:57:05.381][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:05.382][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:05.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.390][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.391][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:05.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:05.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.397][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:05.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:05.400][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.401][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:05.522][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-03-24 21:57:05.526][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-03-24 21:57:05.528][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-03-24 21:57:05.530][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:57:05.532][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-03-24 21:57:05.652][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-03-24 21:57:05.656][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-03-24 21:57:05.658][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-03-24 21:57:05.659][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:57:05.661][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-03-24 21:57:05.682][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-03-24 21:57:05.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-03-24 21:57:05.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.701][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-03-24 21:57:05.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-03-24 21:57:05.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.720][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.722][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.723][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.724][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.725][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.727][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.728][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.729][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.731][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.735][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.736][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:05.741][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:05.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:05.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:05.795][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-03-24 21:57:05.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:05.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:05.850][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-03-24 21:57:10.464][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-03-24 21:57:20.510][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:20.520][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-03-24 21:57:20.564][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-03-24 21:57:21.842][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[2023-03-24 21:57:21.847][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:21.848][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:21.851][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.TRACE[2023-03-24 21:57:22.893][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06).
biodb.DEBUG[2023-03-24 21:57:23.989][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:23.998][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-03-24 21:57:24.014][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-03-24 21:57:24.111][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.DEBUG[2023-03-24 21:57:24.115][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:24.116][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:24.119][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2023-03-24 21:57:25.201][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2023-03-24 21:57:26.286][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:26.295][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-03-24 21:57:26.309][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-03-24 21:57:26.338][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-03-24 21:57:26.339][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-03-24 21:57:26.340][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-03-24 21:57:26.376][biodb::testThat]
biodb.INFO [2023-03-24 21:57:26.379][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-03-24 21:57:26.380][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:26.381][biodb::testThat]
biodb.TRACE[2023-03-24 21:57:26.388][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-03-24 21:57:26.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-03-24 21:57:26.428][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.429][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:26.430][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-03-24 21:57:26.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-03-24 21:57:26.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:26.436][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.437][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:26.441][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.443][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.444][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:26.447][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.448][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.450][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.451][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:26.452][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:26.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:26.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:26.469][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:26.470][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:26.471][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:26.479][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:26.481][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:26.482][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:26.483][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[2023-03-24 21:57:26.535][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[2023-03-24 21:57:26.540][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:26.541][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:26.544][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.TRACE[2023-03-24 21:57:31.346][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01).
biodb.DEBUG[2023-03-24 21:57:41.428][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:41.439][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-03-24 21:57:41.488][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-03-24 21:57:42.668][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-03-24 21:57:42.733][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-03-24 21:57:42.736][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-03-24 21:57:42.738][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-03-24 21:57:42.739][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-03-24 21:57:42.740][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-03-24 21:57:42.742][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-03-24 21:57:42.743][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-03-24 21:57:42.744][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-03-24 21:57:42.765][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:42.766][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:42.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:42.776][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:42.777][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:42.779][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:42.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:57:42.781][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-03-24 21:57:42.785][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:42.787][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:42.788][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-03-24 21:57:43.836][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-03-24 21:57:44.952][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:44.961][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-03-24 21:57:44.974][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-03-24 21:57:44.980][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:44.981][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:44.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:44.990][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:44.991][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:44.992][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:44.994][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:57:44.995][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-03-24 21:57:44.999][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:45.000][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:45.002][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-03-24 21:57:46.066][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-03-24 21:57:47.135][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:57:47.144][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-03-24 21:57:47.158][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-03-24 21:57:47.171][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2023-03-24 21:57:47.177][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-03-24 21:57:47.204][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-03-24 21:57:47.205][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-03-24 21:57:47.208][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:47.209][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:47.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:47.218][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:47.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:47.243][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:47.245][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:57:47.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:57:47.268][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:57:47.269][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.272][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:57:47.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:57:47.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.281][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:57:47.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:57:47.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.287][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:57:47.288][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:57:47.289][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.292][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.297][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.306][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.310][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.312][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.321][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:57:47.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:47.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.326][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:57:47.327][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:47.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.330][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.335][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:57:47.336][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:57:47.338][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.339][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.340][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:57:47.342][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:57:47.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.349][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.351][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.352][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.353][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.363][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:57:47.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.369][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:57:47.370][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.371][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.373][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.374][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.375][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.379][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.381][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.382][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.383][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.384][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:57:47.386][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.387][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.394][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.399][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.409][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.410][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.413][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.414][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.415][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.426][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.432][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.434][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.435][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.437][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:47.474][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:47.476][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:47.477][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:47.486][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:47.487][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:47.489][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:47.490][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:57:47.496][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.499][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.500][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.504][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.511][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:57:47.512][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:57:47.514][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.515][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.516][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:57:47.518][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:57:47.519][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.522][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:57:47.524][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:57:47.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.528][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.529][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.530][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.532][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.533][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:57:47.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.543][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.547][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.548][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:57:47.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.558][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:57:47.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:47.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.563][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:57:47.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:47.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.572][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:57:47.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:57:47.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.577][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.578][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:57:47.580][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:57:47.581][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.582][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.587][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.597][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.602][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:57:47.604][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.605][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.606][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.608][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:57:47.609][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.611][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.612][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.619][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:57:47.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.624][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:57:47.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:57:47.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.629][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.634][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.635][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.645][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.651][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.652][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.656][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.658][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.662][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.695][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.711][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.717][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.718][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.719][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.721][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.722][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:57:47.723][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:57:47.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:47.727][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-03-24 21:57:47.740][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-03-24 21:57:47.742][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:47.743][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:47.744][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:47.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:47.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:47.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:47.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:57:47.757][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.759][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.760][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.761][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.762][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.764][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.765][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.766][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.768][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.769][private$selectFields]
biodb.TRACE[2023-03-24 21:57:47.770][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:57:47.771][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:57:47.773][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.774][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.775][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.777][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.778][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.779][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.781][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.782][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.783][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.784][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.786][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.787][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.788][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.790][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.791][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.792][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:57:47.793][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.799][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.801][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.821][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-03-24 21:57:47.822][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:47.824][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:47.825][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:47.832][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:47.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:47.835][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:47.836][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:57:47.837][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.839][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.840][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.841][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.843][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.847][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.848][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.849][private$selectFields]
biodb.TRACE[2023-03-24 21:57:47.851][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:57:47.852][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:57:47.853][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.855][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.856][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.859][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.860][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.861][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.863][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.864][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.865][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.867][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.868][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.869][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.890][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.891][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.893][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:57:47.894][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.899][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.901][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.902][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.903][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.910][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-03-24 21:57:47.912][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:47.913][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:47.914][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:47.922][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:47.923][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:47.924][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:47.925][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:57:47.927][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.931][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.933][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.938][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.939][private$selectFields]
biodb.TRACE[2023-03-24 21:57:47.940][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:57:47.941][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:57:47.943][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.944][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.945][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.947][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.948][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.949][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.951][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.952][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.953][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.954][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.956][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:57:47.957][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.958][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.960][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.961][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.962][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:57:47.964][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.969][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.970][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:57:47.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:47.980][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-03-24 21:57:47.981][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-03-24 21:57:47.982][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-03-24 21:57:47.994][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-03-24 21:57:47.996][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-03-24 21:57:47.997][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:47.998][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-03-24 21:57:48.001][biodb::testThat]
biodb.INFO [2023-03-24 21:57:48.002][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-03-24 21:57:48.003][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:57:48.004][biodb::testThat]
biodb.TRACE[2023-03-24 21:57:48.008][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-03-24 21:57:48.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-03-24 21:57:48.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:48.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:48.014][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-03-24 21:57:48.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-03-24 21:57:48.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:48.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:48.019][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:48.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:48.024][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:48.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:48.029][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:48.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:57:48.034][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.036][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:57:48.037][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:57:48.038][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:57:48.152][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:57:48.153][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:57:48.154][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:57:48.162][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:57:48.163][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:57:48.164][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:57:48.165][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:57:48.215][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[2023-03-24 21:57:48.219][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:57:48.220][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:57:48.223][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.TRACE[2023-03-24 21:57:52.686][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375).
biodb.DEBUG[2023-03-24 21:58:01.847][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:58:01.857][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-03-24 21:58:01.903][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-03-24 21:58:03.352][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-03-24 21:58:03.383][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:03.384][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:03.386][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:03.393][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:03.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:03.396][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:03.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:03.414][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.415][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.417][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.418][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.419][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.452][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.454][private$selectFields]
biodb.TRACE[2023-03-24 21:58:03.455][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:58:03.456][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:58:03.457][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.459][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.460][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.462][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.463][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.464][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.466][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.467][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.468][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.469][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.484][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.485][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.487][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.488][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.489][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.490][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:58:03.492][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.493][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.497][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.499][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.500][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.501][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.503][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.504][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.508][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-03-24 21:58:03.509][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:03.511][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:03.512][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:03.519][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:03.520][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:03.521][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:03.523][FUN] Functions in observer BiodbConfig: [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[2023-03-24 21:58:03.524][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.529][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.534][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.536][private$selectFields]
biodb.TRACE[2023-03-24 21:58:03.537][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:58:03.538][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:58:03.539][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.541][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.542][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.543][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.545][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.546][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.547][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.550][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.551][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.552][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.554][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.555][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.557][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.559][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:58:03.560][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.563][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.564][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.565][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.567][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.568][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.569][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.570][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.576][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-03-24 21:58:03.578][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:03.579][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:03.580][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:03.588][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:03.589][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:03.591][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:03.592][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:03.593][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.595][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.596][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.599][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.600][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.602][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.603][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.604][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.606][private$selectFields]
biodb.TRACE[2023-03-24 21:58:03.607][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:58:03.608][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:58:03.610][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.611][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.612][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.614][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.615][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.617][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.618][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.620][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.621][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.623][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.624][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:03.625][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.627][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.630][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.631][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:58:03.633][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.636][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.637][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.639][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.645][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:03.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.651][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-03-24 21:58:03.653][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-03-24 21:58:03.654][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-03-24 21:58:03.666][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-03-24 21:58:03.668][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-03-24 21:58:03.669][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-03-24 21:58:03.674][biodb::testThat]
biodb.INFO [2023-03-24 21:58:03.675][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-03-24 21:58:03.676][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:58:03.678][biodb::testThat]
biodb.TRACE[2023-03-24 21:58:03.682][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-03-24 21:58:03.684][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-03-24 21:58:03.685][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.688][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-03-24 21:58:03.690][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-03-24 21:58:03.691][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.692][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.694][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.706][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.709][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.710][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:03.712][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.713][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:03.714][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:03.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:58:03.729][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:03.731][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:03.732][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:03.740][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:03.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:03.743][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:03.744][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:58:03.818][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-03-24 21:58:03.822][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-03-24 21:58:03.824][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-03-24 21:58:03.825][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:58:03.926][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-03-24 21:58:05.055][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-03-24 21:58:05.057][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:05.058][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:05.059][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:05.067][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:05.068][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:05.069][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:05.070][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:05.072][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.077][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.082][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.083][private$selectFields]
biodb.TRACE[2023-03-24 21:58:05.084][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:58:05.085][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:58:05.086][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.088][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.089][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.090][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.091][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.092][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.094][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.095][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.096][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.097][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.099][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.100][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.101][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.102][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.103][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.105][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:58:05.106][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.107][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.111][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.116][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.117][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.118][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.121][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-03-24 21:58:05.123][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:05.124][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:05.125][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:05.132][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:05.134][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:05.135][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:05.136][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[2023-03-24 21:58:05.137][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.139][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.140][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.141][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.142][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.147][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.148][private$selectFields]
biodb.TRACE[2023-03-24 21:58:05.150][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:58:05.151][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:58:05.152][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.153][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.154][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.156][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.157][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.158][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.159][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.162][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.163][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.164][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.165][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.167][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.168][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.169][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.170][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:58:05.172][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.177][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.178][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.179][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.180][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.182][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.183][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.187][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-03-24 21:58:05.188][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:05.190][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:05.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:05.198][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:05.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:05.200][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:05.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:05.203][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.208][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.210][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.211][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.213][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.214][private$selectFields]
biodb.TRACE[2023-03-24 21:58:05.216][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-03-24 21:58:05.217][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:58:05.218][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.219][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.221][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.222][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.223][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.225][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.226][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.227][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.228][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.230][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.231][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:58:05.232][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.233][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.235][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.236][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.237][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-03-24 21:58:05.238][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.243][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.245][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.246][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.247][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.248][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:05.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:05.253][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-03-24 21:58:05.255][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-03-24 21:58:05.256][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-03-24 21:58:05.282][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-03-24 21:58:05.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-03-24 21:58:05.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:05.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-03-24 21:58:05.288][biodb::testThat]
biodb.INFO [2023-03-24 21:58:05.289][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-03-24 21:58:05.291][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:58:05.292][biodb::testThat]
biodb.DEBUG[2023-03-24 21:58:05.294][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-03-24 21:58:05.295][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-03-24 21:58:05.297][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-03-24 21:58:05.299][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-03-24 21:58:05.300][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-03-24 21:58:05.302][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-03-24 21:58:05.303][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-03-24 21:58:05.304][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-03-24 21:58:05.305][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-03-24 21:58:05.323][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:05.324][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:05.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:05.332][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:05.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:05.335][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:05.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:58:05.337][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-03-24 21:58:05.341][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:05.342][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:05.344][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:06.417][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:06.418][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:06.419][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:06.421][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:07.604][private$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[2023-03-24 21:58:07.606][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:07.607][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:07.609][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:08.642][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:08.643][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:08.645][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:08.646][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:09.814][private$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[2023-03-24 21:58:09.815][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:09.817][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:09.818][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:10.849][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:10.850][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:10.852][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:10.853][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:12.020][private$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[2023-03-24 21:58:12.022][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:12.023][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:12.025][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:13.068][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:13.069][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:13.071][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:13.072][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:14.293][private$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[2023-03-24 21:58:14.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:14.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:14.297][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:15.364][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:15.366][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:15.368][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:15.369][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:16.444][private$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[2023-03-24 21:58:16.446][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:16.447][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:16.449][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:17.495][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:17.497][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:17.498][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:17.499][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:18.670][private$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[2023-03-24 21:58:18.671][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:18.672][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:18.674][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:19.714][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:19.715][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:19.717][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:19.718][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:20.898][private$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[2023-03-24 21:58:20.899][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:20.901][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:20.903][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:21.944][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:21.946][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:21.947][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:21.949][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:23.120][private$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[2023-03-24 21:58:23.122][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:23.123][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:23.125][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:24.152][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:24.154][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:24.155][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:24.157][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:25.331][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:25.332][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:25.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:25.335][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-03-24 21:58:26.305][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:26.306][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:26.308][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-03-24 21:58:26.309][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-03-24 21:58:27.489][private$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[2023-03-24 21:58:27.500][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-03-24 21:58:27.505][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-03-24 21:58:27.530][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-03-24 21:58:27.532][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-03-24 21:58:27.534][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:27.535][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:27.537][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:27.545][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:27.546][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:27.548][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:27.549][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:27.552][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:27.553][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:27.555][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.556][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.557][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:27.559][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:27.560][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.563][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:27.565][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:27.566][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.567][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.569][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:27.570][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:27.572][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.573][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.574][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:27.576][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:27.577][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.578][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.580][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:27.581][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:27.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.586][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:27.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:27.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.590][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:27.591][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:27.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:27.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:27.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:58:27.597][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-03-24 21:58:27.598][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-03-24 21:58:27.608][biodb::testThat]
biodb.INFO [2023-03-24 21:58:27.609][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-03-24 21:58:27.610][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:58:27.612][biodb::testThat]
biodb.DEBUG[2023-03-24 21:58:27.623][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-03-24 21:58:27.624][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-03-24 21:58:27.626][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-03-24 21:58:27.628][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-03-24 21:58:27.630][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-03-24 21:58:27.631][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-03-24 21:58:27.633][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-03-24 21:58:27.634][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-03-24 21:58:27.636][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-03-24 21:58:27.637][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-03-24 21:58:27.642][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:27.644][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:27.645][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:27.653][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:27.654][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:27.656][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:27.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:58:27.659][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-03-24 21:58:27.662][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:27.664][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:27.666][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:28.698][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:28.700][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:28.701][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[2023-03-24 21:58:28.703][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:29.922][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:29.924][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:29.925][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:29.927][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:30.969][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:30.970][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:30.971][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[2023-03-24 21:58:30.973][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:32.143][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:32.145][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:32.146][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:32.148][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:33.191][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:33.192][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:33.194][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[2023-03-24 21:58:33.195][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:34.363][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:34.364][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:34.366][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:34.368][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:35.381][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:35.383][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:35.384][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[2023-03-24 21:58:35.385][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:36.555][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:36.556][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:36.558][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:36.559][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:37.600][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:37.601][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:37.603][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[2023-03-24 21:58:37.604][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:38.776][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:38.778][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:38.779][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:38.781][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:39.823][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:39.825][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:39.826][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[2023-03-24 21:58:39.828][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:40.998][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:41.000][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:41.001][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:41.003][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:42.019][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:42.021][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:42.022][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[2023-03-24 21:58:42.024][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:43.202][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:43.203][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:43.205][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:43.207][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:44.223][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:44.224][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:44.225][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[2023-03-24 21:58:44.227][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:45.397][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:45.398][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:45.399][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:45.401][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:46.424][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:46.426][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:46.427][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[2023-03-24 21:58:46.429][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:47.599][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:47.601][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:47.602][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:47.604][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-03-24 21:58:48.601][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-03-24 21:58:48.603][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-03-24 21:58:48.604][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[2023-03-24 21:58:48.606][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-03-24 21:58:49.777][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-03-24 21:58:49.779][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:49.780][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:49.781][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:49.790][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:49.792][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:49.793][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:49.794][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:58:49.796][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-03-24 21:58:49.800][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:49.802][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:49.804][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-03-24 21:58:50.803][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-03-24 21:58:51.965][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:58:51.975][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-03-24 21:58:51.989][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-03-24 21:58:52.004][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGB.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA08040013.tsv"
biodb.DEBUG[2023-03-24 21:58:52.009][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-03-24 21:58:52.035][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-03-24 21:58:52.037][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-03-24 21:58:52.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:52.041][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:52.042][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:52.050][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:52.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:52.053][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:52.054][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:52.057][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.068][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.070][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.071][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:58:52.074][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:58:52.075][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:58:52.077][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:58:52.085][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:58:52.086][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:58:52.088][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:58:52.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:58:52.095][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.100][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.101][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.103][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.111][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:58:52.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:58:52.114][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.117][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:58:52.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:58:52.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.126][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:58:52.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:58:52.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.131][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.133][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:58:52.134][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:58:52.135][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.142][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:58:52.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:58:52.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.147][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.148][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:58:52.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:58:52.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.158][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:58:52.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:58:52.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.165][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:58:52.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:58:52.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.174][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:58:52.176][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:58:52.177][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.181][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:58:52.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:58:52.184][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.185][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.191][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:58:52.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:52.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.197][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:58:52.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:58:52.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.202][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.207][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:58:52.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:58:52.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.213][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:58:52.215][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:58:52.217][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.218][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.224][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.225][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.232][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.233][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.235][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.241][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:58:52.242][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.244][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.247][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:58:52.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.253][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.255][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.256][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.259][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.265][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:58:52.267][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.268][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.270][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.275][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.277][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.278][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.281][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.287][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.293][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.295][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.296][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.297][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.299][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:58:52.301][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:58:52.302][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.303][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.309][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.310][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.315][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.319][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.320][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.323][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.325][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.326][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.328][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:58:52.329][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.332][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.334][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.335][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.337][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.338][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.344][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.345][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.348][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.354][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.357][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.358][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.359][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.361][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.362][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.364][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.365][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.367][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.368][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.371][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.373][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.374][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.377][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.380][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.383][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.389][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:58:52.394][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:58:52.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:58:52.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:58:52.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:58:52.400][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-03-24 21:58:52.401][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-03-24 21:58:52.402][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-03-24 21:58:52.418][biodb::testThat]
biodb.INFO [2023-03-24 21:58:52.420][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-03-24 21:58:52.421][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:58:52.423][biodb::testThat]
biodb.INFO [2023-03-24 21:58:52.452][biodb::testThat]
biodb.INFO [2023-03-24 21:58:52.453][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-03-24 21:58:52.455][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:58:52.456][biodb::testThat]
biodb.INFO [2023-03-24 21:58:52.466][biodb::testThat]
biodb.INFO [2023-03-24 21:58:52.467][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-03-24 21:58:52.469][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:58:52.470][biodb::testThat]
biodb.DEBUG[2023-03-24 21:58:52.493][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[2023-03-24 21:58:52.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:58:52.498][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:58:52.500][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-03-24 21:58:57.016][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-03-24 21:59:06.041][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:06.052][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-03-24 21:59:06.097][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-03-24 21:59:07.470][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:07.472][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:07.473][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:07.475][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:07.476][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:07.478][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:07.479][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:07.480][ef$get] fields variable is a list.
biodb.INFO [2023-03-24 21:59:07.483][biodb::testThat]
biodb.INFO [2023-03-24 21:59:07.484][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-03-24 21:59:07.485][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:59:07.487][biodb::testThat]
biodb.ERROR[2023-03-24 21:59:07.507][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-03-24 21:59:07.530][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-03-24 21:59:07.545][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-03-24 21:59:07.547][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-03-24 21:59:07.549][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-03-24 21:59:07.550][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-03-24 21:59:07.551][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:07.552][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:07.554][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.555][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.556][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.558][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-03-24 21:59:07.573][biodb::testContext]
biodb.INFO [2023-03-24 21:59:07.574][biodb::testContext] ********************************************************************************
biodb.INFO [2023-03-24 21:59:07.576][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-03-24 21:59:07.577][biodb::testContext] ********************************************************************************
biodb.INFO [2023-03-24 21:59:07.578][biodb::testContext]
biodb.INFO [2023-03-24 21:59:07.585][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-03-24 21:59:07.587][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-03-24 21:59:07.592][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:59:07.594][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-03-24 21:59:07.595][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-03-24 21:59:07.596][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.600][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-03-24 21:59:07.602][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-03-24 21:59:07.603][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.605][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.606][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.607][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-03-24 21:59:07.609][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-03-24 21:59:07.610][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.611][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.613][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[2023-03-24 21:59:07.614][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-03-24 21:59:07.615][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-03-24 21:59:07.617][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-03-24 21:59:07.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.621][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.622][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-03-24 21:59:07.624][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-03-24 21:59:07.625][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-03-24 21:59:07.626][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.629][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".
biodb.DEBUG[2023-03-24 21:59:07.630][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-03-24 21:59:07.632][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-03-24 21:59:07.633][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.636][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.637][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-03-24 21:59:07.639][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-03-24 21:59:07.640][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-03-24 21:59:07.642][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.646][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-03-24 21:59:07.647][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-03-24 21:59:07.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.653][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-03-24 21:59:07.654][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-03-24 21:59:07.656][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-03-24 21:59:07.657][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.660][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.661][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-03-24 21:59:07.662][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-03-24 21:59:07.664][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-03-24 21:59:07.665][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-03-24 21:59:07.667][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-03-24 21:59:07.668][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-03-24 21:59:07.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.672][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.673][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-03-24 21:59:07.675][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-03-24 21:59:07.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.678][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.680][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-03-24 21:59:07.681][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-03-24 21:59:07.683][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.684][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.685][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.686][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-03-24 21:59:07.688][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-03-24 21:59:07.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.692][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[2023-03-24 21:59:07.693][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-03-24 21:59:07.694][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-03-24 21:59:07.696][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.697][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.698][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.700][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-03-24 21:59:07.701][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-03-24 21:59:07.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.705][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.706][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-03-24 21:59:07.707][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-03-24 21:59:07.712][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-03-24 21:59:07.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.717][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-03-24 21:59:07.718][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-03-24 21:59:07.720][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-03-24 21:59:07.721][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.725][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-03-24 21:59:07.727][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.729][self$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[2023-03-24 21:59:07.730][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.732][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:07.733][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.734][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.736][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.737][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.738][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:59:07.740][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:07.741][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.743][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-03-24 21:59:07.744][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:07.745][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.747][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.748][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:59:07.748][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:59:07.748][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-03-24 21:59:07.748][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-03-24 21:59:07.748][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-03-24 21:59:07.750][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:07.751][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.752][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.754][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:07.755][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.756][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.758][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.759][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.760][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:07.762][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:07.763][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.764][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.766][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-03-24 21:59:07.768][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.770][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-03-24 21:59:07.771][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.773][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:07.774][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.776][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.777][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.778][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.780][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-03-24 21:59:07.781][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:07.783][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.784][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-03-24 21:59:07.786][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:07.787][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.788][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.790][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:59:07.790][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:59:07.790][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-03-24 21:59:07.790][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-03-24 21:59:07.790][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-03-24 21:59:07.791][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:07.793][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.794][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.795][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:07.797][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.798][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.799][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.801][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.802][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:07.803][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:07.805][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.806][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.808][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-03-24 21:59:07.810][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.811][self$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[2023-03-24 21:59:07.813][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.814][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:07.816][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.817][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.818][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.820][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.821][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:59:07.822][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:07.824][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.825][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-03-24 21:59:07.827][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:07.828][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.829][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.831][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.832][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:07.833][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.835][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.836][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:07.837][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.839][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.840][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.841][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.843][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:07.844][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:07.845][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.847][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.848][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-03-24 21:59:07.851][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.852][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-03-24 21:59:07.854][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.855][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:07.856][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.858][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.859][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.860][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.862][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-03-24 21:59:07.863][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:07.865][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.866][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-03-24 21:59:07.867][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:07.869][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.870][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:07.871][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.873][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:07.874][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.875][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.877][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:07.878][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:07.879][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:07.881][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:07.882][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.883][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:07.885][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:07.886][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:07.887][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:07.889][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:59:07.890][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.892][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.893][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.897][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.898][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.899][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.900][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.902][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.903][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.904][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.905][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.910][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.911][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.916][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.922][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.925][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.926][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.927][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.928][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[2023-03-24 21:59:07.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.932][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.933][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.934][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[2023-03-24 21:59:07.935][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.936][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.938][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.939][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.940][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.941][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.942][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.944][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.945][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.946][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:07.947][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.988][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.992][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[2023-03-24 21:59:07.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:07.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:07.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:07.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:07.998][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[2023-03-24 21:59:08.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.004][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.006][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.008][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.010][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.012][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.013][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.016][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.022][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.024][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.026][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.029][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.035][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[2023-03-24 21:59:08.036][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-03-24 21:59:08.038][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-03-24 21:59:08.040][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-03-24 21:59:08.042][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-03-24 21:59:08.044][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-03-24 21:59:08.046][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-03-24 21:59:08.047][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-03-24 21:59:08.049][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-03-24 21:59:08.051][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-03-24 21:59:08.053][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-03-24 21:59:08.055][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-03-24 21:59:08.057][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-03-24 21:59:08.059][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-03-24 21:59:08.061][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-03-24 21:59:08.062][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-03-24 21:59:08.064][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-03-24 21:59:08.066][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-03-24 21:59:08.068][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-03-24 21:59:08.070][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-03-24 21:59:08.072][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-03-24 21:59:08.074][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-03-24 21:59:08.075][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-03-24 21:59:08.077][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-03-24 21:59:08.079][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-03-24 21:59:08.081][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-03-24 21:59:08.083][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-03-24 21:59:08.085][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-03-24 21:59:08.087][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-03-24 21:59:08.089][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-03-24 21:59:08.090][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-03-24 21:59:08.092][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-03-24 21:59:08.094][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-03-24 21:59:08.096][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-03-24 21:59:08.098][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-03-24 21:59:08.100][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-03-24 21:59:08.101][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-03-24 21:59:08.103][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-03-24 21:59:08.105][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-03-24 21:59:08.107][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-03-24 21:59:08.109][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-03-24 21:59:08.111][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-03-24 21:59:08.113][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-03-24 21:59:08.115][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-03-24 21:59:08.117][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-03-24 21:59:08.118][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-03-24 21:59:08.120][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-03-24 21:59:08.122][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-03-24 21:59:08.124][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-03-24 21:59:08.126][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-03-24 21:59:08.128][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-03-24 21:59:08.130][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-03-24 21:59:08.132][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-03-24 21:59:08.134][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-03-24 21:59:08.135][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-03-24 21:59:08.137][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-03-24 21:59:08.139][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-03-24 21:59:08.141][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-03-24 21:59:08.143][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-03-24 21:59:08.145][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-03-24 21:59:08.147][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-03-24 21:59:08.149][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-03-24 21:59:08.150][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-03-24 21:59:08.152][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-03-24 21:59:08.154][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-03-24 21:59:08.156][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-03-24 21:59:08.158][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-03-24 21:59:08.160][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-03-24 21:59:08.162][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-03-24 21:59:08.164][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-03-24 21:59:08.166][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-03-24 21:59:08.168][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-03-24 21:59:08.169][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-03-24 21:59:08.171][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-03-24 21:59:08.173][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-03-24 21:59:08.175][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-03-24 21:59:08.177][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-03-24 21:59:08.179][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-03-24 21:59:08.181][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-03-24 21:59:08.183][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-03-24 21:59:08.185][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-03-24 21:59:08.187][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-03-24 21:59:08.189][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-03-24 21:59:08.190][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-03-24 21:59:08.192][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-03-24 21:59:08.194][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-03-24 21:59:08.196][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:59:08.197][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.198][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.200][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.207][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.210][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.212][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.213][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.218][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.221][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.224][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.226][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.227][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.228][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.234][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.236][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.237][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.238][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.239][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.240][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.242][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.243][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[2023-03-24 21:59:08.244][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.248][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.249][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.251][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.252][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.254][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.255][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.260][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.261][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.262][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.263][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.268][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.269][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.272][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.274][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.277][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[2023-03-24 21:59:08.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.288][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.291][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.292][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.294][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.295][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.296][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.302][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.304][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.305][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.306][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.307][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.308][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.311][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.312][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.313][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.314][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.316][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.317][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.319][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.321][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.322][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.323][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.325][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.331][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.334][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.336][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.337][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:08.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:08.340][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:08.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:08.342][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:08.344][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:08.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:08.347][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-03-24 21:59:08.349][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:59:08.351][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:08.353][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-03-24 21:59:08.354][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:08.355][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:08.357][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:08.358][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:08.359][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:08.361][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:08.362][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:59:08.363][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:08.365][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:08.366][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-03-24 21:59:08.368][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-03-24 21:59:08.369][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-03-24 21:59:08.370][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:08.372][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:59:08.372][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:59:08.373][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:08.374][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:08.376][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:08.377][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:08.378][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:08.380][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:08.381][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:08.382][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-03-24 21:59:08.382][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-03-24 21:59:08.384][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:08.385][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:08.386][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:08.388][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:08.389][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-03-24 21:59:08.391][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-03-24 21:59:08.396][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:59:08.397][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-03-24 21:59:08.399][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:59:08.401][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-03-24 21:59:08.402][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-03-24 21:59:08.404][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-03-24 21:59:08.405][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-03-24 21:59:08.407][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-03-24 21:59:08.409][biodb::testThat]
biodb.INFO [2023-03-24 21:59:08.410][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-03-24 21:59:08.411][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:59:08.413][biodb::testThat]
biodb.DEBUG[2023-03-24 21:59:08.418][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.DEBUG[2023-03-24 21:59:08.423][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:59:08.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:59:08.427][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-03-24 21:59:09.531][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[2023-03-24 21:59:10.648][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:10.658][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-03-24 21:59:10.673][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-03-24 21:59:10.690][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[2023-03-24 21:59:10.695][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:59:10.696][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:59:10.699][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-03-24 21:59:11.769][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty).
biodb.DEBUG[2023-03-24 21:59:12.863][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:12.873][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-03-24 21:59:12.888][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-03-24 21:59:12.903][biodb::testThat]
biodb.INFO [2023-03-24 21:59:12.905][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-03-24 21:59:12.906][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:59:12.907][biodb::testThat]
biodb.INFO [2023-03-24 21:59:12.945][biodb::testThat]
biodb.INFO [2023-03-24 21:59:12.947][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-03-24 21:59:12.948][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:59:12.949][biodb::testThat]
biodb.DEBUG[2023-03-24 21:59:12.954][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-03-24 21:59:12.958][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:59:12.960][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:59:12.962][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-03-24 21:59:13.883][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-03-24 21:59:14.790][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:14.800][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-03-24 21:59:14.816][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-03-24 21:59:14.827][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[2023-03-24 21:59:14.831][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-03-24 21:59:14.833][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-03-24 21:59:14.835][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:59:14.836][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-03-24 21:59:14.844][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[2023-03-24 21:59:14.848][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:59:14.850][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:59:14.852][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-03-24 21:59:15.763][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001).
biodb.DEBUG[2023-03-24 21:59:16.693][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:16.703][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-03-24 21:59:16.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-03-24 21:59:16.730][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.DEBUG[2023-03-24 21:59:16.734][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:59:16.736][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:59:16.738][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-03-24 21:59:18.410][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-03-24 21:59:20.690][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:20.741][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-03-24 21:59:20.759][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-03-24 21:59:20.913][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[2023-03-24 21:59:20.918][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-03-24 21:59:20.920][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-03-24 21:59:20.922][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.TRACE[2023-03-24 21:59:22.668][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6).
biodb.DEBUG[2023-03-24 21:59:24.910][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-03-24 21:59:24.920][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-03-24 21:59:24.938][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-03-24 21:59:25.081][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-03-24 21:59:25.083][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-03-24 21:59:25.084][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-03-24 21:59:25.085][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-03-24 21:59:25.087][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.088][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.089][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.090][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.092][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.093][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-03-24 21:59:25.099][biodb::testContext]
biodb.INFO [2023-03-24 21:59:25.100][biodb::testContext] ********************************************************************************
biodb.INFO [2023-03-24 21:59:25.101][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-03-24 21:59:25.102][biodb::testContext] ********************************************************************************
biodb.INFO [2023-03-24 21:59:25.104][biodb::testContext]
biodb.INFO [2023-03-24 21:59:25.110][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-03-24 21:59:25.112][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-03-24 21:59:25.117][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:59:25.119][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-03-24 21:59:25.120][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-03-24 21:59:25.121][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.122][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.124][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.125][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-03-24 21:59:25.127][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-03-24 21:59:25.128][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.129][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.131][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.132][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-03-24 21:59:25.133][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-03-24 21:59:25.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.137][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[2023-03-24 21:59:25.139][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-03-24 21:59:25.140][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-03-24 21:59:25.142][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-03-24 21:59:25.143][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.144][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.146][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.147][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-03-24 21:59:25.148][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-03-24 21:59:25.150][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-03-24 21:59:25.151][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.155][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-03-24 21:59:25.157][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-03-24 21:59:25.158][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.159][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.160][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.162][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-03-24 21:59:25.163][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-03-24 21:59:25.165][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-03-24 21:59:25.166][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.168][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.170][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-03-24 21:59:25.171][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-03-24 21:59:25.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.174][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.176][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-03-24 21:59:25.178][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-03-24 21:59:25.179][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-03-24 21:59:25.180][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.182][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.183][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.184][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-03-24 21:59:25.186][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-03-24 21:59:25.187][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-03-24 21:59:25.189][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-03-24 21:59:25.190][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-03-24 21:59:25.192][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-03-24 21:59:25.193][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.195][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.197][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-03-24 21:59:25.198][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-03-24 21:59:25.200][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.201][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.202][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.203][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-03-24 21:59:25.205][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-03-24 21:59:25.206][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.207][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.210][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-03-24 21:59:25.212][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-03-24 21:59:25.213][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.214][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.215][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.217][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-03-24 21:59:25.218][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-03-24 21:59:25.219][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.221][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.222][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.223][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-03-24 21:59:25.225][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-03-24 21:59:25.226][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.229][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.230][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-03-24 21:59:25.231][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-03-24 21:59:25.235][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-03-24 21:59:25.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.241][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-03-24 21:59:25.242][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-03-24 21:59:25.244][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-03-24 21:59:25.245][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.246][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.247][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.249][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-03-24 21:59:25.252][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.253][self$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[2023-03-24 21:59:25.254][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.256][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:25.257][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.259][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.260][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.261][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.263][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:59:25.264][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:25.266][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.267][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-03-24 21:59:25.269][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:25.270][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.271][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.273][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:59:25.273][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:59:25.273][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-03-24 21:59:25.273][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-03-24 21:59:25.273][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-03-24 21:59:25.274][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:25.276][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.277][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.278][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:25.280][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.281][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.282][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.284][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.285][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:25.286][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:25.288][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.289][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.291][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-03-24 21:59:25.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.295][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-03-24 21:59:25.296][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.298][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:25.299][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.300][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.302][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.303][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.305][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-03-24 21:59:25.306][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:25.308][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.309][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-03-24 21:59:25.310][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:25.312][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.313][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.315][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:59:25.315][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:59:25.315][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-03-24 21:59:25.315][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-03-24 21:59:25.315][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-03-24 21:59:25.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:25.318][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.319][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.320][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:25.321][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.323][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.324][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.326][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.327][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:25.328][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:25.329][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.331][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.333][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-03-24 21:59:25.335][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.337][self$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[2023-03-24 21:59:25.338][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.339][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:25.341][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.342][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.344][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.345][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.346][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:59:25.348][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:25.349][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.351][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-03-24 21:59:25.352][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:25.354][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.355][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.356][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.358][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:25.359][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.360][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.362][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:25.363][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.365][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.366][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.367][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.369][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:25.370][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:25.371][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.373][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.374][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-03-24 21:59:25.377][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.378][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-03-24 21:59:25.380][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.381][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:25.382][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.384][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.385][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.387][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.388][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-03-24 21:59:25.390][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:25.391][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.392][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-03-24 21:59:25.394][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:25.395][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.397][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.398][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.400][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:25.401][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.402][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.404][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:25.405][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.406][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.408][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.409][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.410][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:25.412][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:25.413][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.415][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.416][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:59:25.418][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.419][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.420][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.423][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.426][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.427][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.428][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.429][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.431][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.432][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.433][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.435][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.436][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.438][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.440][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.441][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.442][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.475][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.482][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.483][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.484][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.485][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.487][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.488][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[2023-03-24 21:59:25.489][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.490][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.492][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.493][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.494][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[2023-03-24 21:59:25.495][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.497][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.498][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.499][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.500][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.502][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.503][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.504][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.505][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.506][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.508][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.509][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.511][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.516][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.517][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.518][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.519][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.520][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.521][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.524][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.525][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.526][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.527][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.528][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.530][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.531][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.532][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.533][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.534][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.535][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.537][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.538][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.539][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.541][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.542][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.544][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.545][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.546][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.547][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.548][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.549][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.550][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.553][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[2023-03-24 21:59:25.554][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-03-24 21:59:25.556][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-03-24 21:59:25.558][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-03-24 21:59:25.560][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-03-24 21:59:25.561][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-03-24 21:59:25.563][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-03-24 21:59:25.565][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-03-24 21:59:25.567][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-03-24 21:59:25.569][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-03-24 21:59:25.570][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-03-24 21:59:25.572][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-03-24 21:59:25.574][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-03-24 21:59:25.576][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-03-24 21:59:25.578][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-03-24 21:59:25.580][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-03-24 21:59:25.581][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-03-24 21:59:25.583][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-03-24 21:59:25.585][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-03-24 21:59:25.587][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-03-24 21:59:25.588][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-03-24 21:59:25.590][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-03-24 21:59:25.592][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-03-24 21:59:25.594][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-03-24 21:59:25.596][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-03-24 21:59:25.597][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-03-24 21:59:25.599][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-03-24 21:59:25.601][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-03-24 21:59:25.603][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-03-24 21:59:25.605][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-03-24 21:59:25.607][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-03-24 21:59:25.608][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-03-24 21:59:25.610][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-03-24 21:59:25.612][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-03-24 21:59:25.614][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-03-24 21:59:25.616][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-03-24 21:59:25.617][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-03-24 21:59:25.619][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-03-24 21:59:25.621][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-03-24 21:59:25.623][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-03-24 21:59:25.625][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-03-24 21:59:25.626][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-03-24 21:59:25.628][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-03-24 21:59:25.630][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-03-24 21:59:25.632][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-03-24 21:59:25.634][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-03-24 21:59:25.636][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-03-24 21:59:25.637][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-03-24 21:59:25.639][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-03-24 21:59:25.641][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-03-24 21:59:25.643][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-03-24 21:59:25.645][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-03-24 21:59:25.647][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-03-24 21:59:25.649][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-03-24 21:59:25.650][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-03-24 21:59:25.652][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-03-24 21:59:25.654][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-03-24 21:59:25.656][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-03-24 21:59:25.658][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-03-24 21:59:25.660][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-03-24 21:59:25.662][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-03-24 21:59:25.664][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-03-24 21:59:25.665][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-03-24 21:59:25.667][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-03-24 21:59:25.669][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-03-24 21:59:25.671][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-03-24 21:59:25.673][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-03-24 21:59:25.675][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-03-24 21:59:25.676][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-03-24 21:59:25.678][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-03-24 21:59:25.680][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-03-24 21:59:25.682][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-03-24 21:59:25.684][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-03-24 21:59:25.686][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-03-24 21:59:25.688][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-03-24 21:59:25.689][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-03-24 21:59:25.691][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-03-24 21:59:25.693][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-03-24 21:59:25.695][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-03-24 21:59:25.697][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-03-24 21:59:25.699][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-03-24 21:59:25.701][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-03-24 21:59:25.702][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-03-24 21:59:25.704][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-03-24 21:59:25.706][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-03-24 21:59:25.708][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-03-24 21:59:25.710][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-03-24 21:59:25.711][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.713][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.714][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.716][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.718][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.722][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.723][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.724][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.726][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.727][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.731][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[2023-03-24 21:59:25.732][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.733][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.734][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.739][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.743][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.745][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.749][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.750][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.751][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.759][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.761][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.762][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.765][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.767][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.768][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.770][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.771][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.773][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.776][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.777][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.778][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.781][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.782][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.783][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.784][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.787][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.788][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.789][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.790][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.792][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.793][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.794][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.795][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.798][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[2023-03-24 21:59:25.799][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.800][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.801][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.803][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.805][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.806][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.809][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.810][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.812][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.813][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.814][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.819][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.820][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.822][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.824][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.826][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.834][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.835][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.836][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[2023-03-24 21:59:25.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.839][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.840][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.841][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.843][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.844][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.845][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.846][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.848][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.849][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.850][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.851][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.853][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.854][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.855][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-03-24 21:59:25.857][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:25.858][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:25.859][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:25.860][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:25.862][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:25.863][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-03-24 21:59:25.866][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R-devel_2023-03-12_r83975-bin/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-03-24 21:59:25.868][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:59:25.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.872][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.875][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-03-24 21:59:25.876][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.878][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.879][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.881][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.882][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-03-24 21:59:25.884][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-03-24 21:59:25.885][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.886][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-03-24 21:59:25.888][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-03-24 21:59:25.889][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-03-24 21:59:25.891][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-03-24 21:59:25.892][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-03-24 21:59:25.892][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-03-24 21:59:25.894][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-03-24 21:59:25.895][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.896][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.898][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-03-24 21:59:25.899][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-03-24 21:59:25.900][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-03-24 21:59:25.902][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-03-24 21:59:25.903][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-03-24 21:59:25.903][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-03-24 21:59:25.905][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-03-24 21:59:25.906][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-03-24 21:59:25.907][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-03-24 21:59:25.909][self$setPropertyValue]
biodb.DEBUG[2023-03-24 21:59:25.910][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-03-24 21:59:25.914][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-03-24 21:59:25.919][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:59:25.920][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-03-24 21:59:25.922][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-03-24 21:59:25.924][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-03-24 21:59:25.925][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-03-24 21:59:25.927][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-03-24 21:59:25.929][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-03-24 21:59:25.930][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-03-24 21:59:25.932][biodb::testThat]
biodb.INFO [2023-03-24 21:59:25.933][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2023-03-24 21:59:25.935][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-03-24 21:59:25.936][biodb::testThat]
biodb.DEBUG[2023-03-24 21:59:25.942][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-03-24 21:59:25.948][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-03-24 21:59:25.950][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-03-24 21:59:25.979][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-03-24 21:59:26.072][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-03-24 21:59:27.193][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-03-24 21:59:27.195][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-03-24 21:59:27.197][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-03-24 21:59:27.199][cch$loadFileContent] file.exist = [2]: "TRUE, TRUE".
biodb.TRACE[2023-03-24 21:59:27.202][loadFileContents] Loaded 2 files from cache: [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-03-24 21:59:27.203][conn$getEntryContent] 2 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-03-24 21:59:27.227][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-03-24 21:59:27.229][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-03-24 21:59:27.231][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:59:27.233][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:27.234][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:27.242][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:27.243][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:27.244][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:27.246][FUN] Functions in observer BiodbConfig: [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[2023-03-24 21:59:27.252][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.258][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.261][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.262][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.267][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.273][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.275][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.276][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.283][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:59:27.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:59:27.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.289][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:59:27.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:59:27.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.293][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.294][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.296][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.297][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.300][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.310][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.315][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.317][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.318][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.320][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.325][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:59:27.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.329][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.330][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:59:27.332][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.333][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.335][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.340][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.343][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.344][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.346][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.347][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.355][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.356][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.358][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.359][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.361][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.362][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.370][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:59:27.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.376][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:59:27.378][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.379][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.380][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.382][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.384][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.385][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.386][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.388][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.391][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.392][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.394][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:59:27.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.403][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.409][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.411][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.412][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.413][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.415][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.416][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.421][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.424][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.425][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.426][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.428][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.429][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.436][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.438][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.439][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.440][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.442][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.444][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.445][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.446][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.448][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.449][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.454][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.455][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.458][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.459][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.461][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.462][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.464][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.465][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.467][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.468][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.470][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.471][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.473][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.474][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.475][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:59:27.481][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:59:27.482][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:27.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:27.491][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:27.493][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:27.494][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:27.495][FUN] Functions in observer BiodbConfig: [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[2023-03-24 21:59:27.502][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.503][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.505][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.506][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.509][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.517][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.522][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.523][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.525][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.526][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.533][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:59:27.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-03-24 21:59:27.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.539][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:59:27.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-03-24 21:59:27.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.545][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.548][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.549][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.551][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.552][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.554][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.555][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.561][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.562][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.564][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.565][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.567][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.576][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:59:27.578][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.579][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.581][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.582][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-03-24 21:59:27.584][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.585][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.592][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.597][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.602][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.607][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.608][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.610][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.611][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.613][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.622][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:59:27.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.629][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-03-24 21:59:27.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.632][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.633][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.634][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.645][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.646][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-03-24 21:59:27.648][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.656][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.659][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.662][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.664][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.668][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.674][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.689][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.692][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.724][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.729][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.735][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.743][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.744][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.745][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.751][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.754][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-03-24 21:59:27.756][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-03-24 21:59:27.759][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-03-24 21:59:27.761][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:59:27.762][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:27.763][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:27.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:27.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:27.773][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:27.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:59:27.777][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:59:27.779][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:59:27.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.783][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:59:27.784][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:59:27.785][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.787][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.788][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-03-24 21:59:27.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-03-24 21:59:27.791][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.792][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.793][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-03-24 21:59:27.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-03-24 21:59:27.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.798][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.799][private$selectFields] Fields none
biodb.TRACE[2023-03-24 21:59:27.800][private$selectFields]
biodb.TRACE[2023-03-24 21:59:27.801][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-03-24 21:59:27.803][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:59:27.804][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:59:27.805][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.807][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.808][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.809][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.811][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.812][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.814][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.815][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.816][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.818][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.819][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.820][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.822][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.823][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.824][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.826][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.827][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.829][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.830][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.831][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.833][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.834][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.835][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.837][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.838][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.839][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.841][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.842][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.843][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.845][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.846][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.847][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.849][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.850][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.851][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.853][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.854][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.856][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.857][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.858][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.860][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.861][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.862][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.864][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.865][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.866][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.868][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.869][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.870][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.872][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.873][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.875][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.876][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.877][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.879][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.880][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.881][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.883][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.884][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.885][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.887][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.888][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.889][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.891][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.892][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:59:27.893][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:59:27.895][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.896][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.899][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.900][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.902][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.903][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.904][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.906][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.907][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.908][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.910][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.911][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.913][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.914][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.915][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.917][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.918][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:27.919][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.921][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.922][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:27.924][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:27.925][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.926][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.928][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:27.929][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:27.930][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.932][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.933][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.934][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:27.936][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.937][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.938][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-03-24 21:59:27.940][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.941][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.945][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.951][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:27.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:27.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.957][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.962][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.968][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:27.971][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.972][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.974][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.979][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.985][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:27.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.990][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.992][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.993][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:27.995][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:27.996][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:27.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.001][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.006][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.007][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.013][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.018][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.024][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.030][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.035][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.041][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.044][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.045][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.047][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.048][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.052][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.064][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.065][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.067][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.068][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.069][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.082][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-03-24 21:59:28.084][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-03-24 21:59:28.085][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:28.087][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:28.094][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:28.095][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:28.097][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:28.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-03-24 21:59:28.101][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:59:28.102][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:59:28.103][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.106][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-03-24 21:59:28.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-03-24 21:59:28.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.112][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-03-24 21:59:28.113][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-03-24 21:59:28.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.117][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-03-24 21:59:28.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-03-24 21:59:28.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.122][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.123][private$selectFields] Fields none
biodb.TRACE[2023-03-24 21:59:28.124][private$selectFields]
biodb.TRACE[2023-03-24 21:59:28.126][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-03-24 21:59:28.127][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-03-24 21:59:28.128][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:59:28.130][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:28.131][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:28.133][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.134][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.135][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.137][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.138][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.140][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.141][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.142][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.144][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.145][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.147][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.148][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.151][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.152][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.154][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.155][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.156][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.158][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.159][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.161][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.162][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.163][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.165][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.166][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.168][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.169][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.170][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.172][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.173][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.175][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:28.176][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:28.177][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.179][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.180][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.182][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.183][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.184][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.186][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.187][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.189][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.190][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.191][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.212][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.213][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.215][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.216][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.217][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.219][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.220][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.221][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.223][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.224][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.225][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.227][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.228][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.229][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.231][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.232][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.234][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.235][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.236][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.238][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:59:28.239][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-03-24 21:59:28.240][ef$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:28.242][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:28.243][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.244][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.246][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.247][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.248][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.250][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.251][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.252][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.254][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.255][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.256][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.258][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.259][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.260][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.262][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.263][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.264][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.266][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.267][ef$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.269][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.270][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.271][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.272][ef$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.274][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.275][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.276][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.278][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.279][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.281][ef$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.282][ef$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.283][private$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[2023-03-24 21:59:28.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:28.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:28.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.289][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:28.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:28.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.296][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-03-24 21:59:28.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-03-24 21:59:28.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.300][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.301][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.304][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.305][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.307][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.309][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.312][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-03-24 21:59:28.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.318][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.319][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.320][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.323][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.328][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.330][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-03-24 21:59:28.331][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.332][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.334][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.335][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.339][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.341][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.342][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.343][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.345][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-03-24 21:59:28.348][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.349][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.350][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.352][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.353][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.355][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.356][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.357][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.359][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.360][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.361][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.363][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-03-24 21:59:28.364][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.365][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.367][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.368][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.371][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.372][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.374][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.375][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.376][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.378][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-03-24 21:59:28.379][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-03-24 21:59:28.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.383][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.388][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.389][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.390][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.395][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-03-24 21:59:28.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-03-24 21:59:28.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.400][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.406][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.407][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.411][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-03-24 21:59:28.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-03-24 21:59:28.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-03-24 21:59:28.422][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000002, 137783, 42607281, N-(3S-hydroxydecanoyl)-L-serine, 275.173274, ...].
biodb.DEBUG[2023-03-24 21:59:28.423][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-03-24 21:59:28.425][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-03-24 21:59:28.429][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-03-24 21:59:28.430][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-03-24 21:59:28.432][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-03-24 21:59:28.433][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-03-24 21:59:28.434][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-03-24 21:59:28.435][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-03-24 21:59:28.437][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-03-24 21:59:28.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-03-24 21:59:28.439][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-03-24 21:59:28.440][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 168 ]
>
> proc.time()
user system elapsed
36.751 2.116 153.453
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 3.499 | 0.303 | 7.656 | |
| LipidmapsStructureEntry | 0.497 | 0.193 | 0.691 | |