| Back to Multiple platform build/check report for BioC 3.17 |
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This page was generated on 2023-04-12 10:55:22 -0400 (Wed, 12 Apr 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) | x86_64 | 4.3.0 alpha (2023-04-03 r84154) | 4547 |
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) | x86_64 | R Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences" | 4333 |
| 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: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/biodbLipidmaps.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. Note: If "R CMD check" recently failed on the Linux builder over a missing dependency, add the missing dependency to "Suggests" in your DESCRIPTION file. See the Renviron.bioc for details. |
| Package 198/2207 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
| biodbLipidmaps 1.5.0 (landing page) Pierrick Roger
| nebbiolo1 | Linux (Ubuntu 22.04.1 LTS) / x86_64 | OK | OK | OK | |||||||||
| nebbiolo2 | Linux (Ubuntu 20.04.5 LTS) / x86_64 | 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: 2023-04-11 18:52:52 -0400 (Tue, 11 Apr 2023) |
| EndedAt: 2023-04-11 18:56:14 -0400 (Tue, 11 Apr 2023) |
| EllapsedTime: 202.1 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 version 4.3.0 alpha (2023-04-03 r84154)
* using platform: x86_64-pc-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 loading without being on the library search path ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’
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/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 version 4.3.0 alpha (2023-04-03 r84154)
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: x86_64-pc-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 [2023-04-11 18:53:33.673][biodb::testContext]
biodb.INFO [2023-04-11 18:53:33.676][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:33.677][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-11 18:53:33.678][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:53:33.679][biodb::testContext]
biodb.INFO [2023-04-11 18:53:33.698][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:33.700][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:33.709][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:33.711][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:53:33.712][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:53:33.713][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.714][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.715][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.716][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:53:33.737][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:53:33.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.740][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.741][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.742][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:53:33.743][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:53:33.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.751][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.752][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:53:33.753][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:53:33.754][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:53:33.755][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.756][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.757][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.759][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:53:33.760][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:53:33.761][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:53:33.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.764][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.765][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:53:33.766][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:53:33.767][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.768][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.769][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.770][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:53:33.771][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:53:33.773][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:53:33.773][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.774][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.775][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.777][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:53:33.778][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:53:33.779][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.780][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.781][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[2023-04-11 18:53:33.782][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:53:33.783][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:53:33.784][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:53:33.785][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.786][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.787][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.788][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:33.789][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:53:33.790][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:53:33.791][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:53:33.793][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:53:33.794][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:53:33.795][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.796][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.797][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[2023-04-11 18:53:33.798][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:53:33.799][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:53:33.800][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.801][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.802][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.803][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:53:33.804][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:53:33.805][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.806][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.807][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.808][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:53:33.809][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:53:33.810][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.811][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.812][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.813][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:53:33.815][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:53:33.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.819][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:53:33.820][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:53:33.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.824][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:53:33.825][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:53:33.829][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:53:33.830][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.831][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.832][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.833][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:53:33.834][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:53:33.835][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:53:33.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:33.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:33.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:33.844][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:53:33.885][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:33.925][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:53:33.927][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.930][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:33.931][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:33.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:33.936][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:33.938][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:33.939][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:33.940][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.942][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:53:33.943][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:33.945][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:33.946][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.947][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:33.947][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:33.947][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:33.947][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:33.947][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:33.949][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:33.950][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:33.952][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:33.953][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:33.954][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:33.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:33.957][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:33.958][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:33.960][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:33.961][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:33.963][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:33.964][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:33.966][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:53:33.969][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:33.970][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:33.972][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.973][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:33.975][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.976][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:33.977][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:33.979][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:33.980][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:33.982][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:33.983][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.985][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:53:33.986][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:33.987][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:33.989][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:33.990][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:33.990][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:33.990][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:53:33.990][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:53:33.990][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:53:33.992][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:33.993][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:33.994][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:33.995][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:33.997][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:33.998][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.000][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.001][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.002][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:34.004][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:34.005][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.006][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.008][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:53:34.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:53:34.014][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.015][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:34.016][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.017][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.019][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.020][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.021][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:34.023][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:34.024][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.025][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:53:34.027][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:34.028][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.029][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.031][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.032][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:34.033][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:34.034][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.035][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:34.037][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:34.038][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.039][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.040][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.041][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:34.043][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:34.044][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.045][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.047][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:53:34.049][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.051][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:53:34.052][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.053][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:34.055][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.056][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.057][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.059][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.060][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:53:34.061][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:34.062][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.064][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:53:34.065][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:34.066][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.067][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.069][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.070][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:34.071][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:34.072][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.074][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:34.075][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:34.076][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.077][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.079][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.080][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:34.081][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:34.082][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.083][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.088][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:34.089][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.090][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.092][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.092][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.093][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.094][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.095][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.096][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.098][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.099][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.100][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.101][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.103][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.104][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.105][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[2023-04-11 18:53:34.106][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.108][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.109][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.110][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.111][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.113][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.115][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.116][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.117][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.118][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.119][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.120][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.122][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.123][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.124][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[2023-04-11 18:53:34.125][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.126][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.127][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.128][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.129][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.130][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.131][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.133][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.135][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.136][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.137][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.138][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.139][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[2023-04-11 18:53:34.140][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.141][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.142][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.143][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.144][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.145][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.145][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.146][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.147][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.148][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.149][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.150][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.151][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.152][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.153][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.154][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.155][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.156][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.159][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.160][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.161][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.162][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.163][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.164][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.165][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.166][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.167][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.168][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[2023-04-11 18:53:34.169][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.170][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.171][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.172][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.173][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.174][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:53:34.180][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:53:34.182][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:53:34.183][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:53:34.185][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:53:34.186][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:53:34.188][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:34.189][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:34.191][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:53:34.192][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:53:34.194][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:53:34.195][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:53:34.197][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:53:34.198][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:53:34.200][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:53:34.201][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:34.203][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:53:34.204][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:53:34.206][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:53:34.207][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:53:34.209][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:53:34.211][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:53:34.212][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:53:34.214][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:53:34.215][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:53:34.217][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:53:34.219][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:53:34.220][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:53:34.222][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:53:34.224][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:53:34.234][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:53:34.237][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:53:34.238][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:53:34.240][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:53:34.242][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:53:34.243][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:53:34.244][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:53:34.246][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:53:34.247][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:53:34.249][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:53:34.250][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:53:34.251][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:53:34.253][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:53:34.254][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:53:34.256][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:53:34.257][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:53:34.258][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:53:34.260][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:53:34.261][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:53:34.262][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:53:34.264][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:53:34.265][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:53:34.266][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:53:34.267][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:53:34.269][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:53:34.270][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:53:34.271][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:53:34.273][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:53:34.274][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:53:34.276][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:53:34.277][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:53:34.279][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:53:34.280][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:53:34.281][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:53:34.283][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:53:34.284][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:53:34.285][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:53:34.287][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:53:34.288][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:53:34.289][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:53:34.291][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:53:34.292][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:53:34.293][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:53:34.295][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:53:34.296][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:53:34.298][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:53:34.299][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:53:34.300][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:53:34.302][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:53:34.303][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:53:34.304][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:53:34.306][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:53:34.307][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:53:34.313][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:53:34.315][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:53:34.319][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:53:34.320][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.321][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.322][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.323][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.328][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.329][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.334][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.335][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.340][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.342][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.343][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.346][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.347][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.348][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.351][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.352][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.353][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.353][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.355][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.357][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.359][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.360][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.361][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.363][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.364][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.366][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.369][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.370][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.371][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.372][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.373][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.375][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.376][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.377][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.378][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.379][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.DEBUG[2023-04-11 18:53:34.380][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.382][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.384][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.385][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.386][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.387][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.388][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.389][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.390][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.391][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.392][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.395][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.397][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.399][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.400][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.401][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.402][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.403][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.404][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.405][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.406][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.407][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.408][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.409][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.409][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.410][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.411][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.412][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.414][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.414][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.415][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.416][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.417][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.419][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.420][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.421][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.422][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.423][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.424][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.425][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.426][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.427][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.428][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.429][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.430][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.430][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.431][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.433][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.434][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:53:34.435][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:53:34.436][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.437][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.437][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.438][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.439][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.440][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[2023-04-11 18:53:34.443][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-11 18:53:34.455][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:53:34.457][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.459][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.460][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.461][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:53:34.462][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.464][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.465][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.466][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.467][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:53:34.468][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:53:34.469][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.470][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-11 18:53:34.471][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-11 18:53:34.472][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-11 18:53:34.474][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:53:34.475][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:53:34.475][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:53:34.476][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:53:34.477][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:34.478][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.479][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:53:34.480][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:53:34.481][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:53:34.482][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:53:34.483][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:53:34.483][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-11 18:53:34.484][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:53:34.485][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:53:34.486][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:53:34.487][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:53:34.503][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-11 18:53:34.505][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:53:34.535][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:53:34.537][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-11 18:53:34.543][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:53:34.548][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-11 18:53:34.553][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-11 18:53:34.554][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-11 18:53:34.556][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-11 18:53:34.557][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-11 18:53:34.579][biodb::testThat]
biodb.INFO [2023-04-11 18:53:34.580][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-11 18:53:34.581][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:34.582][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:34.588][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/testref/entry-lipidmaps.structure-LMFA00000001-content.tsv".
biodb.DEBUG[2023-04-11 18:53:34.593][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:34.598][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-11 18:53:34.607][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:34.608][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:34.609][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:34.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:34.628][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:34.630][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:34.631][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:34.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.646][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.647][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.648][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.649][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.670][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.672][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:34.673][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.674][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.675][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:34.676][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:34.677][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.678][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.680][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:34.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:34.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.684][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:34.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:34.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.715][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:34.717][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:34.718][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.719][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.724][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:34.725][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:34.726][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.727][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.729][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:34.730][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:34.731][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.732][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.737][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:53:34.738][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:34.739][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.740][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.741][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:53:34.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:34.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.749][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:34.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:34.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.753][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:34.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:34.756][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.757][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.761][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.765][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.773][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:53:34.775][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.776][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.780][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:53:34.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.783][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.784][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.786][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.792][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.798][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:53:34.800][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.855][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.859][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.896][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.901][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.905][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:34.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:34.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.913][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:34.914][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:34.915][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.916][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.917][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:34.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:34.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.921][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.925][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:34.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:34.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.929][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.933][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.937][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.944][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.945][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.946][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.948][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.952][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:34.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:34.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:34.956][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-11 18:53:34.963][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:34.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:34.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.967][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:34.968][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:34.969][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.970][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.971][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:34.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:34.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:34.976][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:34.978][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:34.979][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:34.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.009][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.012][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.041][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.043][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.045][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.063][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.066][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.067][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.069][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.077][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.081][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.082][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.084][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.090][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.096][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.098][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.103][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.109][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.111][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.125][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.126][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.136][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.137][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.143][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.144][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.145][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.146][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.147][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.148][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.149][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.151][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.152][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.153][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.154][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.155][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.164][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.171][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.172][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.173][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.177][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.178][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.179][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.179][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.180][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.192][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.196][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.200][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.201][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.204][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.205][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.206][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.207][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.208][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.221][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.226][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.227][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.228][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.229][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.230][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.234][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.235][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.236][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.237][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.238][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.251][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.255][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.257][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.258][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.260][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.261][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.262][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.263][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.264][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.265][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.266][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.267][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.268][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.280][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.281][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.282][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.283][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.285][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.289][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.290][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.291][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.292][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.293][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.294][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.295][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.296][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.298][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.309][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.310][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.312][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.313][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.318][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.320][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.321][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.322][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.328][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.329][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.330][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.331][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.337][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.338][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.340][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.346][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.347][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.349][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.355][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.356][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.357][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.358][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:35.365][biodb::testThat]
biodb.INFO [2023-04-11 18:53:35.366][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-11 18:53:35.367][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:35.368][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:35.418][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-04-11 18:53:35.428][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:53:35.434][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-04-11 18:53:35.435][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:35.437][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-04-11 18:53:35.438][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:53:35.489][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:53:35.491][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-11 18:53:35.493][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:53:35.494][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:53:35.495][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:53:35.501][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:53:35.502][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:53:35.503][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:53:35.504][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:53:35.508][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.510][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.511][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.512][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.513][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.514][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.515][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.516][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.521][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.522][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.523][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.524][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.526][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:53:35.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.534][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:35.535][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:53:35.536][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.537][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.538][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:35.539][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:53:35.540][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.541][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.543][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.544][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.545][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.546][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.547][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.548][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:53:35.549][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.550][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.555][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.560][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.561][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:53:35.562][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.563][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.568][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:53:35.569][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.570][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.571][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.573][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:53:35.574][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:35.575][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.576][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.581][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.582][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.583][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.585][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:53:35.586][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:53:35.587][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.588][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.593][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.598][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.599][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.600][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.601][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.605][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:53:35.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.610][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:53:35.611][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.612][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.613][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.614][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.615][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.616][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.617][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.618][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.620][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.621][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.622][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.623][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:53:35.624][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.625][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.626][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.631][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.632][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.633][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.634][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.637][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.640][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.641][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.644][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.649][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.661][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.665][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.667][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.668][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.669][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.670][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.674][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.678][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:53:35.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.681][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.682][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.686][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.687][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.688][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.689][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.690][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.691][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.692][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.693][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.697][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.698][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.699][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.700][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:53:35.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:53:35.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:35.710][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-11 18:53:35.711][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-11 18:53:35.712][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-11 18:53:35.713][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.714][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.715][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-11 18:53:35.716][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-11 18:53:35.717][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.718][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.719][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-11 18:53:35.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-11 18:53:35.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:35.729][biodb::testThat]
biodb.INFO [2023-04-11 18:53:35.730][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-11 18:53:35.731][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:35.732][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:35.736][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.737][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.738][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.739][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:35.740][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-04-11 18:53:35.770][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.771][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:35.780][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:35.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:35.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:35.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:35.786][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-11 18:53:35.802][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[2023-04-11 18:53:35.826][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:35.828][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:35.830][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-04-11 18:53:37.377][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-04-11 18:53:38.468][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:38.477][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-04-11 18:53:38.504][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-04-11 18:53:38.510][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-04-11 18:53:38.525][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:38.526][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:38.527][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.528][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:38.531][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.532][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-11 18:53:38.533][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:38.534][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:38.583][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:38.585][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:38.586][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.587][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.588][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:38.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:38.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.592][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:38.593][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:38.594][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.595][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:38.709][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-11 18:53:38.713][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:38.730][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-11 18:53:38.732][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:38.734][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-04-11 18:53:38.760][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.761][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-11 18:53:38.762][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:38.763][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:38.792][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.794][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.795][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.796][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.802][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:38.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:38.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.806][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:38.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:38.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.857][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.863][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:53:38.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.868][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:38.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:53:38.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:38.872][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:38.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:53:38.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:38.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:38.880][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.881][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-11 18:53:38.882][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:38.883][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.889][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.890][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-11 18:53:38.891][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:38.892][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.897][biodb::testThat]
biodb.INFO [2023-04-11 18:53:38.899][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-11 18:53:38.900][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:38.901][biodb::testThat]
biodb.DEBUG[2023-04-11 18:53:38.905][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-04-11 18:53:39.845][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-04-11 18:53:40.389][biodb::testThat]
biodb.INFO [2023-04-11 18:53:40.390][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-11 18:53:40.391][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:40.393][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:40.437][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:40.438][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:40.440][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.442][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.443][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:40.445][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:40.447][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.448][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:53:40.451][biodb::testThat]
biodb.INFO [2023-04-11 18:53:40.452][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-04-11 18:53:40.454][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:53:40.455][biodb::testThat]
biodb.TRACE[2023-04-11 18:53:40.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:40.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:40.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:40.487][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:40.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:40.491][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:53:40.492][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:53:40.494][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:40.495][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:40.608][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.INFO [2023-04-11 18:53:40.612][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.DEBUG[2023-04-11 18:53:40.630][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:40.632][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:40.649][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-04-11 18:53:41.436][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-04-11 18:53:42.248][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:53:42.264][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-04-11 18:53:42.288][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-04-11 18:53:42.405][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-11 18:53:42.409][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:53:42.411][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-11 18:53:42.412][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:53:42.414][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-04-11 18:53:42.431][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:53:42.432][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:53:42.433][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.434][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:42.457][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:42.459][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:53:42.460][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.461][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:42.475][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.477][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.478][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:42.480][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.481][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.482][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.483][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:42.484][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:42.488][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:53:42.493][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.494][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:53:42.495][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:53:42.496][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:53:42.541][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-04-11 18:53:42.546][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:42.547][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:42.549][private$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[2023-04-11 18:53:46.717][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[2023-04-11 18:53:58.281][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2023-04-11 18:53:58.291][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2023-04-11 18:53:58.298][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-04-11 18:53:58.323][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-04-11 18:53:59.329][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-04-11 18:53:59.333][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:53:59.334][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:53:59.336][private$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[2023-04-11 18:54:00.082][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[2023-04-11 18:54:01.168][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:01.178][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-04-11 18:54:01.195][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-04-11 18:54:01.290][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[2023-04-11 18:54:01.294][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:01.295][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:01.298][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2023-04-11 18:54:02.035][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2023-04-11 18:54:02.829][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:02.844][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-04-11 18:54:02.862][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-04-11 18:54:02.894][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:02.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:02.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:02.918][biodb::testThat]
biodb.INFO [2023-04-11 18:54:02.920][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-11 18:54:02.921][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:02.923][biodb::testThat]
biodb.TRACE[2023-04-11 18:54:02.930][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:54:02.931][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:54:02.932][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:02.933][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:03.004][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:03.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:03.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:03.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:03.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.017][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:03.020][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:03.021][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.022][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:03.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:03.026][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:03.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:03.031][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.033][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:03.034][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:03.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:03.047][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:03.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:03.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:03.057][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:03.058][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:03.059][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:03.060][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:03.107][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-04-11 18:54:03.111][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:03.112][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:03.114][private$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[2023-04-11 18:54:06.996][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[2023-04-11 18:54:18.449][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:18.460][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-04-11 18:54:18.482][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-04-11 18:54:19.405][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-04-11 18:54:19.453][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-11 18:54:19.455][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-04-11 18:54:19.457][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-11 18:54:19.458][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:54:19.459][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:54:19.460][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:54:19.461][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:54:19.462][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:54:19.478][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:19.479][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:19.483][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:19.493][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:19.494][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:19.496][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:19.497][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:19.498][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-04-11 18:54:19.502][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:19.504][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:19.505][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-04-11 18:54:20.242][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-04-11 18:54:21.010][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:21.018][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-04-11 18:54:21.029][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-04-11 18:54:21.034][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:21.035][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:21.036][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:21.041][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:21.042][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:21.043][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:21.044][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:21.046][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-04-11 18:54:21.048][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:21.049][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:21.051][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-04-11 18:54:21.793][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-04-11 18:54:22.561][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:22.567][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-04-11 18:54:22.578][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-04-11 18:54:22.587][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2023-04-11 18:54:22.591][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:54:22.610][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-11 18:54:22.611][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-11 18:54:22.613][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:22.614][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:22.615][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:22.620][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:22.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:22.622][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.623][FUN] Functions in observer BiodbConfig: [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[2023-04-11 18:54:22.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.650][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.651][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.652][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.653][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.654][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.655][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.656][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:22.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:22.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:22.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:22.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.670][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:54:22.671][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:54:22.672][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.673][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.674][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:22.675][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:22.676][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.677][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.678][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.679][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.680][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.682][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.683][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.684][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.692][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.698][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:54:22.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:22.700][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.701][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.702][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:54:22.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:22.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.705][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.709][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:22.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:22.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.712][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:22.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:22.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.716][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.719][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.720][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.721][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.722][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.723][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.724][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.725][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.726][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.731][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:54:22.732][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.733][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.734][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.735][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:54:22.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.746][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:54:22.747][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.748][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.749][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.757][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.761][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.765][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.772][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.777][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.779][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.779][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:22.783][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:22.784][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:22.785][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:22.803][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:22.804][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:22.805][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.806][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.TRACE[2023-04-11 18:54:22.810][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.812][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.816][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.817][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.821][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:54:22.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:54:22.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.825][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:54:22.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:54:22.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.829][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:22.830][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:54:22.831][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.832][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.833][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.834][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.835][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.836][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.837][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.838][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:54:22.839][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.840][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.844][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.846][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.847][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:54:22.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.854][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:54:22.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:22.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.858][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:54:22.859][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:22.860][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.861][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.865][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:22.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:22.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.869][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:54:22.870][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:54:22.871][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.872][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.876][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.880][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.887][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:54:22.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.890][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:54:22.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.894][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.898][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:54:22.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.902][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:54:22.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:54:22.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.908][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.910][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.911][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.912][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.913][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.914][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.915][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.916][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.917][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.920][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.924][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.928][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.929][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.930][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.930][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.932][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.933][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.933][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.934][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.938][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.954][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.958][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.959][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.960][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.961][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.962][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.963][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.964][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.965][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.966][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.967][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.968][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.969][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:22.970][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:22.971][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:22.972][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.973][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:22.974][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-04-11 18:54:22.984][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:22.985][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:22.986][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:22.987][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:22.992][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:22.993][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:22.994][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:22.995][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:22.996][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.997][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:22.998][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:22.999][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.000][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.001][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.002][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.003][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.004][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.005][private$selectFields]
biodb.TRACE[2023-04-11 18:54:23.006][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:23.007][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:23.008][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.009][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.010][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.011][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.012][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.013][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.014][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.015][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.015][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.016][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.017][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.018][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.019][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.020][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.021][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.022][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:23.023][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.025][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.026][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.027][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.029][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.030][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.031][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.032][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.033][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.034][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.044][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-11 18:54:23.045][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:23.046][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.047][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.052][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.053][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.054][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.055][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:23.056][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.060][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.064][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.065][private$selectFields]
biodb.TRACE[2023-04-11 18:54:23.066][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:23.067][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:23.068][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.069][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.070][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.071][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.072][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.073][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.075][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.076][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.077][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.078][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.079][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.080][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.081][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.082][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.083][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.084][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:23.085][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.089][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.107][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.110][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.111][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-11 18:54:23.112][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:23.113][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.114][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.120][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.121][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.122][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:23.124][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.127][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.131][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.132][private$selectFields]
biodb.TRACE[2023-04-11 18:54:23.133][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:23.134][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:23.135][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.136][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.137][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.138][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.138][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.139][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.140][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.141][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.142][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.143][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.144][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:23.145][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.146][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.147][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.148][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.149][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:23.150][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.151][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.152][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.153][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.153][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.155][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.156][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.157][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.158][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:23.159][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.160][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.161][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-11 18:54:23.162][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:23.163][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:23.173][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:23.174][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:23.175][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.176][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:23.178][biodb::testThat]
biodb.INFO [2023-04-11 18:54:23.179][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-11 18:54:23.180][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:23.181][biodb::testThat]
biodb.TRACE[2023-04-11 18:54:23.185][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:54:23.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:54:23.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.189][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:23.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:23.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.193][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.194][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.195][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.196][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.197][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.198][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.199][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.200][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.201][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.202][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.202][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.203][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:23.204][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:23.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:23.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:23.307][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:23.308][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:23.309][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:23.315][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:23.316][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:23.316][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:23.317][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:23.354][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2023-04-11 18:54:23.358][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:23.359][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:23.360][private$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[2023-04-11 18:54:27.269][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[2023-04-11 18:54:38.612][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:54:38.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-04-11 18:54:38.645][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-04-11 18:54:39.787][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:39.815][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:39.817][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:39.818][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:39.825][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:39.827][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:39.828][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:39.829][FUN] Functions in observer BiodbConfig: [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[2023-04-11 18:54:39.844][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.845][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.850][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.851][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.875][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.876][private$selectFields]
biodb.TRACE[2023-04-11 18:54:39.878][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:39.879][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:39.880][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.881][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.882][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.883][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.884][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.886][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.887][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.889][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.890][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.943][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.944][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.945][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.946][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.947][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.948][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:39.949][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.950][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.951][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.952][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.953][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.954][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.955][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.956][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.957][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.958][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.959][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.960][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.962][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-11 18:54:39.963][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:39.964][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:39.965][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:39.970][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:39.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:39.972][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:39.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:39.974][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.975][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.976][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.977][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.978][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.979][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.980][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.981][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.982][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.983][private$selectFields]
biodb.TRACE[2023-04-11 18:54:39.984][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:39.985][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:39.986][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.987][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.988][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.989][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.990][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.991][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.992][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.993][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.993][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:39.994][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.995][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:39.996][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.997][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:39.998][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:39.999][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.000][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:40.001][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.002][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.003][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.004][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.005][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.006][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.007][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.008][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.009][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.012][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.013][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-11 18:54:40.015][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:40.015][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:40.016][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:40.022][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:40.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:40.024][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:40.025][FUN] Functions in observer BiodbConfig: [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[2023-04-11 18:54:40.026][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.030][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.034][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:40.035][private$selectFields]
biodb.TRACE[2023-04-11 18:54:40.036][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:40.037][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:40.038][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:40.039][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.040][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.041][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.042][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.043][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.044][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.045][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.046][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.047][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:40.048][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:40.049][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.050][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.051][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.052][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.053][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:40.054][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.062][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:40.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.067][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-11 18:54:40.068][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:40.069][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:40.079][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:40.080][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:40.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:40.086][biodb::testThat]
biodb.INFO [2023-04-11 18:54:40.087][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-11 18:54:40.088][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:40.089][biodb::testThat]
biodb.TRACE[2023-04-11 18:54:40.104][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-11 18:54:40.105][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-11 18:54:40.106][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.107][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.108][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:40.110][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-11 18:54:40.111][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.112][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.113][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.115][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.117][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.118][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.119][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.120][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.121][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.122][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.122][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.123][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:40.124][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.125][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:54:40.126][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:40.127][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:40.138][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:40.139][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:40.140][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:40.146][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:40.147][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:40.148][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:40.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:40.190][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[2023-04-11 18:54:40.193][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:54:40.195][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-04-11 18:54:40.196][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:54:40.246][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-04-11 18:54:41.045][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:54:41.048][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:41.049][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:41.050][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:41.055][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:41.056][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:41.057][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:41.058][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:41.059][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.060][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.061][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.062][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.063][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.067][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.068][private$selectFields]
biodb.TRACE[2023-04-11 18:54:41.069][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:41.070][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:41.071][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.072][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.073][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.074][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.075][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.076][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.077][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.078][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.078][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.079][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.080][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.081][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.082][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.083][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.084][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.085][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:41.086][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.087][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.088][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.089][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.090][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.091][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.092][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.093][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.094][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.123][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-11 18:54:41.124][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:41.125][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:41.126][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:41.131][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:41.132][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:41.133][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:41.134][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:41.135][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.139][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.143][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.144][private$selectFields]
biodb.TRACE[2023-04-11 18:54:41.145][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:41.146][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:41.147][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.148][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.149][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.150][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.151][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.151][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.153][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.154][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.155][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.155][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.156][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.157][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.158][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.159][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.160][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.161][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:41.162][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.163][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.164][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.165][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.166][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.167][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.168][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.169][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.170][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.171][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.174][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-11 18:54:41.175][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:41.176][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:41.177][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:41.182][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:41.183][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:41.184][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:41.185][FUN] Functions in observer BiodbConfig: [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[2023-04-11 18:54:41.186][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.190][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.194][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.195][private$selectFields]
biodb.TRACE[2023-04-11 18:54:41.196][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-11 18:54:41.197][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:54:41.198][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.199][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.200][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.201][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.202][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.203][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.204][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.205][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.205][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.206][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.208][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:54:41.208][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.210][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.210][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.211][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.212][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-11 18:54:41.213][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.217][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.221][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:41.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:41.225][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-11 18:54:41.226][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:54:41.227][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-11 18:54:41.248][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:41.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-11 18:54:41.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-11 18:54:41.253][biodb::testThat]
biodb.INFO [2023-04-11 18:54:41.254][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-11 18:54:41.255][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:41.256][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:41.258][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-11 18:54:41.260][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-11 18:54:41.272][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-11 18:54:41.274][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-11 18:54:41.275][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:54:41.276][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:54:41.277][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:54:41.278][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:54:41.279][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:54:41.293][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:41.294][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:41.295][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:41.302][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:41.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:41.304][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:41.305][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:41.306][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-04-11 18:54:41.309][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:41.310][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:41.311][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:41.999][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:42.001][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:42.002][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[2023-04-11 18:54:42.004][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:42.820][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:42.821][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:42.822][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:42.823][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:43.506][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:43.508][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:43.509][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[2023-04-11 18:54:43.510][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:44.319][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:44.321][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:44.322][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:44.324][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:45.013][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:45.015][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:45.017][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[2023-04-11 18:54:45.019][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:45.867][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:45.868][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:45.869][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:45.871][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:46.564][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:46.566][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:46.568][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[2023-04-11 18:54:46.570][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:47.422][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:47.424][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:47.425][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:47.426][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:48.132][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:48.133][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:48.135][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[2023-04-11 18:54:48.136][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:48.947][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:48.949][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:48.950][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:48.951][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:49.638][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:49.640][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:49.641][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[2023-04-11 18:54:49.642][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:50.453][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:50.454][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:50.455][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:50.457][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:51.143][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:51.144][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:51.145][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[2023-04-11 18:54:51.147][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:51.965][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:51.967][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:51.968][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:51.969][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:52.653][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:52.654][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:52.655][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[2023-04-11 18:54:52.657][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:53.503][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:53.505][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:53.507][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:53.509][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:54.224][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:54.226][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:54.227][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[2023-04-11 18:54:54.229][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:55.076][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-11 18:54:55.077][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:55.078][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:55.080][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-11 18:54:55.765][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:55.767][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:55.768][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[2023-04-11 18:54:55.769][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-11 18:54:56.615][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-04-11 18:54:56.623][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-04-11 18:54:56.627][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:54:56.645][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-11 18:54:56.646][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-11 18:54:56.648][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:56.649][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:56.649][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:56.655][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:56.656][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:56.657][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:56.658][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:54:56.659][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:56.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:56.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.662][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.663][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:56.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:54:56.665][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.666][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.667][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:56.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.676][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:56.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.680][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:56.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:56.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.701][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:56.703][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:56.704][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:54:56.706][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:54:56.707][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:54:56.708][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:54:56.709][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:54:56.710][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-11 18:54:56.711][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-11 18:54:56.718][biodb::testThat]
biodb.INFO [2023-04-11 18:54:56.719][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-11 18:54:56.720][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:54:56.721][biodb::testThat]
biodb.DEBUG[2023-04-11 18:54:56.730][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-04-11 18:54:56.731][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-04-11 18:54:56.732][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-11 18:54:56.734][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-04-11 18:54:56.735][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-11 18:54:56.736][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-11 18:54:56.738][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:54:56.739][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:54:56.740][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:54:56.741][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:54:56.745][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:54:56.745][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:54:56.746][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:54:56.752][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:54:56.753][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:54:56.754][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:54:56.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:54:56.756][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-04-11 18:54:56.759][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:56.760][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:56.761][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:54:57.444][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:57.445][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:57.446][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:54:57.447][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:54:58.275][private$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[2023-04-11 18:54:58.277][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:58.279][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:58.281][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:54:59.001][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:54:59.003][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:54:59.004][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:54:59.006][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:54:59.835][private$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[2023-04-11 18:54:59.836][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:54:59.837][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:54:59.839][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:00.542][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:00.543][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:00.545][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:00.546][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:01.381][private$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[2023-04-11 18:55:01.382][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:01.383][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:01.385][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:02.073][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:02.075][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:02.077][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:02.078][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:02.822][private$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[2023-04-11 18:55:02.824][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:02.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:02.828][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:03.543][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:03.545][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:03.547][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:03.548][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:04.297][private$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[2023-04-11 18:55:04.299][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:04.300][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:04.302][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:05.007][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:05.008][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:05.010][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:05.011][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:05.859][private$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[2023-04-11 18:55:05.861][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:05.862][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:05.864][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:06.546][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:06.547][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:06.549][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:06.551][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:07.403][private$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[2023-04-11 18:55:07.405][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:07.407][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:07.450][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:08.153][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:08.154][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:08.155][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:08.156][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:08.967][private$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[2023-04-11 18:55:08.968][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:08.969][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:08.971][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:09.654][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:09.655][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:09.656][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:09.657][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:10.509][private$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[2023-04-11 18:55:10.511][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:10.512][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:10.513][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-11 18:55:11.214][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-11 18:55:11.216][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-11 18:55:11.218][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-11 18:55:11.219][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-11 18:55:12.070][private$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[2023-04-11 18:55:12.071][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:12.072][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:12.073][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:12.079][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:12.080][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:12.081][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:12.082][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:12.083][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-04-11 18:55:12.086][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:12.087][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:12.088][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-04-11 18:55:12.801][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-04-11 18:55:13.563][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:13.571][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-04-11 18:55:13.582][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-04-11 18:55:13.594][private$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[2023-04-11 18:55:13.598][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:55:13.617][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-11 18:55:13.618][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-11 18:55:13.620][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:13.621][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:13.622][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:13.627][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:13.629][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:13.629][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:13.630][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:55:13.632][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.633][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.634][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.635][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.636][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.638][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.639][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.640][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.642][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.643][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:55:13.645][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:13.645][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:13.646][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:13.652][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:13.653][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:13.654][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:13.655][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:55:13.660][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.664][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.672][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:13.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:13.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.676][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:13.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:13.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.684][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:13.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:13.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.688][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:13.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:13.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.696][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:13.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:13.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.700][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:13.702][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:13.703][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.704][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.724][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:13.726][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:13.727][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.728][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.730][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:13.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:13.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.738][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:13.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:13.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.742][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:13.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:13.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.749][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:55:13.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:13.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.753][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:55:13.755][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:13.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.760][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:13.761][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:13.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.764][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:13.765][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:13.766][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.767][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.771][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.772][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.773][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.774][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.775][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.776][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.777][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.778][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.782][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:55:13.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.786][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:55:13.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.790][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.794][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.798][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:55:13.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.805][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.806][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.807][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.808][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.809][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.810][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.811][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.812][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.813][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.814][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.815][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.816][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.817][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.818][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.819][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.820][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.821][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:13.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:13.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.834][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.835][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.837][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.838][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.839][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.840][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:13.841][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.842][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.843][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.847][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.848][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.849][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.850][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.863][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.864][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.865][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.866][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.867][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.868][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.869][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.882][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.883][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.884][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.885][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.886][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.887][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.888][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.889][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.890][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.891][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.894][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.895][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.896][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.897][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:13.898][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:13.899][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:13.900][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:13.901][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:55:13.902][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-04-11 18:55:13.903][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-11 18:55:13.904][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-11 18:55:13.916][biodb::testThat]
biodb.INFO [2023-04-11 18:55:13.917][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-11 18:55:13.918][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:13.919][biodb::testThat]
biodb.INFO [2023-04-11 18:55:13.938][biodb::testThat]
biodb.INFO [2023-04-11 18:55:13.939][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-11 18:55:13.940][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:13.941][biodb::testThat]
biodb.INFO [2023-04-11 18:55:13.948][biodb::testThat]
biodb.INFO [2023-04-11 18:55:13.949][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-11 18:55:13.950][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:13.951][biodb::testThat]
biodb.DEBUG[2023-04-11 18:55:13.954][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-04-11 18:55:13.957][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:13.958][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:13.960][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-04-11 18:55:17.928][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-04-11 18:55:29.421][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:29.428][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-04-11 18:55:29.447][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-04-11 18:55:30.338][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:30.340][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:30.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:30.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:30.344][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:30.345][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:30.346][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:30.347][ef$get] fields variable is a list.
biodb.INFO [2023-04-11 18:55:30.349][biodb::testThat]
biodb.INFO [2023-04-11 18:55:30.350][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-11 18:55:30.351][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:30.352][biodb::testThat]
biodb.ERROR[2023-04-11 18:55:30.370][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-11 18:55:30.391][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-11 18:55:30.404][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:55:30.406][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-11 18:55:30.407][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-11 18:55:30.408][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:55:30.409][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.410][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.411][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.412][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.413][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.414][FUN] Functions in observer BiodbConfig: [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 [2023-04-11 18:55:30.426][biodb::testContext]
biodb.INFO [2023-04-11 18:55:30.427][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:55:30.428][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-04-11 18:55:30.429][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:55:30.430][biodb::testContext]
biodb.INFO [2023-04-11 18:55:30.436][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:55:30.438][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:55:30.442][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:55:30.443][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:55:30.444][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:55:30.445][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.446][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.447][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.448][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:55:30.450][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:55:30.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.452][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.453][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:55:30.455][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:55:30.455][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.456][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.457][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.458][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:55:30.459][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:55:30.460][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:55:30.461][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.462][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.463][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.464][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:55:30.465][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:55:30.467][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:55:30.468][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.469][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.470][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.471][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:55:30.472][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:55:30.473][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.474][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.475][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.476][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:55:30.477][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:55:30.478][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:55:30.479][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.480][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.481][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.482][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:55:30.484][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:55:30.485][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.486][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.487][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[2023-04-11 18:55:30.488][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:55:30.489][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:55:30.511][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:55:30.513][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.514][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.515][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.515][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:55:30.516][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:55:30.517][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:55:30.518][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:55:30.519][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:55:30.520][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:55:30.521][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.522][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.523][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.DEBUG[2023-04-11 18:55:30.524][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:55:30.525][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:55:30.526][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.527][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.527][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.528][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:55:30.529][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:55:30.530][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.531][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.532][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.533][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:55:30.534][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:55:30.535][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.536][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.537][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.538][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:55:30.539][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:55:30.539][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.540][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.541][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[2023-04-11 18:55:30.542][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:55:30.543][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:55:30.544][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.545][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.546][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.546][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:55:30.547][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:55:30.551][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:55:30.551][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.552][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.553][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[2023-04-11 18:55:30.554][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:55:30.555][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:55:30.556][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:55:30.557][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.558][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.559][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.560][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:55:30.562][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.563][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:55:30.564][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.565][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:30.566][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.567][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.567][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.568][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.569][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:55:30.570][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:30.571][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.572][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:55:30.573][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:30.574][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.575][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.576][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:55:30.576][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:55:30.576][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:55:30.576][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:55:30.576][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:55:30.577][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:30.578][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.579][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.580][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:30.581][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.582][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.583][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.584][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.585][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:30.586][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:30.586][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.587][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.589][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:55:30.590][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.591][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:55:30.592][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.593][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:30.594][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.595][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.596][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.597][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.598][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:55:30.599][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:30.600][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.601][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:55:30.602][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:30.603][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.604][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.605][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:55:30.605][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:55:30.605][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:55:30.605][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:55:30.605][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:55:30.606][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:30.607][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.607][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.608][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:30.609][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.610][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.611][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.612][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.613][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:30.614][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:30.615][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.616][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.617][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:55:30.619][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.620][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:55:30.621][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.622][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:30.622][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.623][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.624][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.625][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.626][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:55:30.627][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:30.628][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.629][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:55:30.630][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:30.631][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.632][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.633][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.634][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:30.635][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.636][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.637][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:30.638][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.639][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.640][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.641][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.642][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:30.643][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:30.643][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.656][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.657][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:55:30.659][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.660][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:55:30.661][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.662][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:30.663][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.664][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.665][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.666][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.667][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:55:30.668][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:30.669][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.670][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:55:30.671][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:30.672][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.673][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:30.674][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.675][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:30.676][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.677][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.677][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:30.678][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:30.679][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:30.680][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:30.681][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.682][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:30.683][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:30.684][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:30.685][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:30.686][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:55:30.687][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.688][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.689][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.690][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.690][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.691][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.692][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[2023-04-11 18:55:30.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.695][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.696][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.696][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.697][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.698][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.699][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.700][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.701][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.702][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.703][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.703][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.705][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[2023-04-11 18:55:30.706][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.707][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.708][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.709][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.710][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.711][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.712][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.713][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.714][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[2023-04-11 18:55:30.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.716][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.717][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.718][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.719][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.720][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.721][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.722][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.723][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.724][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.724][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.725][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.726][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.727][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.728][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.729][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.730][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.733][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.734][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.736][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.736][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.737][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.738][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.739][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[2023-04-11 18:55:30.740][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.741][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.742][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.742][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.743][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.745][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.746][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.747][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.748][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.750][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.751][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.752][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.753][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.754][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.754][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.756][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[2023-04-11 18:55:30.757][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.758][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.759][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.760][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.761][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:55:30.763][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:55:30.764][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:55:30.766][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:55:30.767][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:55:30.768][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:55:30.770][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:55:30.771][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:55:30.772][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:55:30.774][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:55:30.775][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:55:30.776][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:55:30.778][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:55:30.779][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:55:30.781][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:55:30.782][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:55:30.783][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:55:30.785][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:55:30.799][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:55:30.800][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:55:30.802][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:55:30.803][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:55:30.804][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:55:30.806][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:55:30.807][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:55:30.808][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:55:30.810][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:55:30.811][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:55:30.813][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:55:30.814][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:55:30.815][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:55:30.817][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:55:30.818][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:55:30.819][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:55:30.821][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:55:30.822][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:55:30.823][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:55:30.825][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:55:30.826][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:55:30.827][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:55:30.828][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:55:30.830][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:55:30.831][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:55:30.832][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:55:30.834][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:55:30.835][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:55:30.836][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:55:30.838][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:55:30.839][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:55:30.840][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:55:30.842][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:55:30.843][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:55:30.844][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:55:30.845][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:55:30.847][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:55:30.848][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:55:30.849][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:55:30.851][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:55:30.852][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:55:30.853][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:55:30.854][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:55:30.856][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:55:30.857][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:55:30.858][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:55:30.860][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:55:30.861][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:55:30.862][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:55:30.864][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:55:30.865][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:55:30.866][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:55:30.868][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:55:30.869][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:55:30.870][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:55:30.872][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:55:30.873][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:55:30.874][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:55:30.876][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:55:30.877][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:55:30.878][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:55:30.880][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:55:30.881][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:55:30.882][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:55:30.884][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:55:30.885][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:55:30.887][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:55:30.888][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:55:30.888][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.889][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.890][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.891][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.892][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.893][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.894][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.894][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.895][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.896][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.897][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.898][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.899][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.900][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.901][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.901][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.902][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.903][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.904][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.905][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.906][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.907][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.908][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.909][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.910][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[2023-04-11 18:55:30.910][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.911][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.912][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.913][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.914][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.915][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.916][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[2023-04-11 18:55:30.917][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.918][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.919][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.919][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.920][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.921][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.922][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[2023-04-11 18:55:30.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.939][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.940][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.940][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.942][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.943][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.944][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.945][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.946][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.947][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.948][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.949][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.950][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.951][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.952][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.953][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.953][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.954][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.955][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.956][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.957][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.958][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.959][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.959][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.960][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.961][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.962][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.963][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.964][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.965][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.966][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.967][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.968][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.969][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.970][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.971][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.972][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.973][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.974][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.975][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.976][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.977][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.978][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.979][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.979][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.980][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.981][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.982][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.985][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.986][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:30.987][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.988][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.990][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.992][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[2023-04-11 18:55:30.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:30.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:30.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:30.995][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:30.996][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:30.997][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:30.998][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[2023-04-11 18:55:30.999][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:31.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:31.001][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:31.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:31.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:31.003][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:31.004][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[2023-04-11 18:55:31.005][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:31.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:31.007][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:31.008][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:31.009][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:31.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:31.010][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[2023-04-11 18:55:31.012][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-11 18:55:31.021][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:55:31.023][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:31.024][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:55:31.025][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:31.026][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:31.027][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:31.028][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:31.029][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:31.030][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:31.031][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:55:31.032][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:31.033][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:31.034][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-11 18:55:31.035][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-11 18:55:31.036][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-11 18:55:31.037][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:31.038][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:55:31.038][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:55:31.039][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:31.040][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:31.041][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:31.042][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:31.043][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:31.044][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:31.045][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:31.046][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:55:31.046][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-11 18:55:31.047][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:31.048][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:31.049][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:31.050][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:31.051][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-11 18:55:31.052][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:55:31.056][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:55:31.057][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-11 18:55:31.058][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:55:31.060][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-11 18:55:31.061][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-11 18:55:31.062][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-11 18:55:31.063][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-11 18:55:31.064][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-11 18:55:31.066][biodb::testThat]
biodb.INFO [2023-04-11 18:55:31.067][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-04-11 18:55:31.068][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:31.069][biodb::testThat]
biodb.DEBUG[2023-04-11 18:55:31.084][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[2023-04-11 18:55:31.089][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:31.090][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:31.091][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-04-11 18:55:31.830][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-04-11 18:55:32.602][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:32.612][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-04-11 18:55:32.628][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-04-11 18:55:32.643][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-04-11 18:55:32.647][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:32.648][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:32.650][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-04-11 18:55:33.385][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[2023-04-11 18:55:34.159][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:34.166][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-04-11 18:55:34.229][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-04-11 18:55:34.239][biodb::testThat]
biodb.INFO [2023-04-11 18:55:34.240][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-04-11 18:55:34.241][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:34.242][biodb::testThat]
biodb.INFO [2023-04-11 18:55:34.267][biodb::testThat]
biodb.INFO [2023-04-11 18:55:34.268][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-04-11 18:55:34.269][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:34.270][biodb::testThat]
biodb.DEBUG[2023-04-11 18:55:34.273][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[2023-04-11 18:55:34.276][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:34.277][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:34.278][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-04-11 18:55:34.847][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-04-11 18:55:35.434][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:35.445][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-04-11 18:55:35.462][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-04-11 18:55:35.472][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-04-11 18:55:35.477][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:55:35.479][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-04-11 18:55:35.481][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:55:35.483][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-04-11 18:55:35.491][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2023-04-11 18:55:35.497][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:35.498][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:35.501][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-04-11 18:55:36.113][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[2023-04-11 18:55:36.748][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:36.755][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-04-11 18:55:36.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-04-11 18:55:36.775][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[2023-04-11 18:55:36.779][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:36.781][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:36.783][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-04-11 18:55:38.120][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-04-11 18:55:42.103][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:42.114][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-04-11 18:55:42.133][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-04-11 18:55:42.252][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2023-04-11 18:55:42.256][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:42.257][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:42.259][private$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[2023-04-11 18:55:43.920][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[2023-04-11 18:55:47.571][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:47.580][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-04-11 18:55:47.593][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-04-11 18:55:47.704][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:55:47.705][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-11 18:55:47.706][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-11 18:55:47.707][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:55:47.708][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:47.709][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:47.710][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.711][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.712][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.713][FUN] Functions in observer BiodbConfig: [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 [2023-04-11 18:55:47.717][biodb::testContext]
biodb.INFO [2023-04-11 18:55:47.718][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:55:47.718][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-04-11 18:55:47.719][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-11 18:55:47.720][biodb::testContext]
biodb.INFO [2023-04-11 18:55:47.725][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:55:47.727][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-11 18:55:47.731][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:55:47.732][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-11 18:55:47.733][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-11 18:55:47.734][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.735][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.735][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.736][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-11 18:55:47.737][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-11 18:55:47.738][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.739][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.740][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.741][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-11 18:55:47.742][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-11 18:55:47.743][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.744][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.745][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.745][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-11 18:55:47.746][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-11 18:55:47.747][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-11 18:55:47.748][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.749][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.750][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.751][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-11 18:55:47.752][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-11 18:55:47.753][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-11 18:55:47.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.755][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.756][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-11 18:55:47.757][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-11 18:55:47.758][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.759][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.760][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.761][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-11 18:55:47.762][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-11 18:55:47.763][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-11 18:55:47.764][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.765][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.766][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.767][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-11 18:55:47.768][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-11 18:55:47.769][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.770][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.771][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.772][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-11 18:55:47.773][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-11 18:55:47.774][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-11 18:55:47.774][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.775][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.776][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.777][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:55:47.778][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-11 18:55:47.779][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-11 18:55:47.780][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-11 18:55:47.781][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-11 18:55:47.782][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-11 18:55:47.801][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.802][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.803][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[2023-04-11 18:55:47.804][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-11 18:55:47.805][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-11 18:55:47.806][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.807][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.808][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.809][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-11 18:55:47.810][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-11 18:55:47.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.814][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-11 18:55:47.815][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-11 18:55:47.815][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.816][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.817][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.818][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-11 18:55:47.819][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-11 18:55:47.820][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.821][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.822][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[2023-04-11 18:55:47.823][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-11 18:55:47.824][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-11 18:55:47.825][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.825][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.826][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.827][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-11 18:55:47.828][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-11 18:55:47.831][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-11 18:55:47.832][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.833][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.834][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.835][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-11 18:55:47.836][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-11 18:55:47.837][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-11 18:55:47.838][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.838][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.839][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.840][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-11 18:55:47.842][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.843][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-11 18:55:47.844][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.845][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:47.846][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.847][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.848][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.849][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.850][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:55:47.851][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:47.852][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.853][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-11 18:55:47.854][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:47.855][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.856][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.857][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:55:47.857][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:55:47.857][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:55:47.857][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:55:47.857][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:55:47.858][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:47.859][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.860][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.860][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:47.861][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.862][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.863][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.864][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.865][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:47.866][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:47.867][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.868][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.869][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-11 18:55:47.871][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.872][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:55:47.873][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.874][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:47.875][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.876][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.877][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.878][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.879][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:55:47.880][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:47.881][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.881][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-11 18:55:47.882][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:47.883][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.884][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.885][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:55:47.885][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:55:47.885][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-11 18:55:47.885][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-11 18:55:47.885][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-11 18:55:47.886][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:47.887][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.888][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.889][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:47.890][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.891][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.892][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.893][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.894][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:47.895][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:47.896][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.897][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.898][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-11 18:55:47.900][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.901][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-11 18:55:47.901][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.902][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:47.903][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.904][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.905][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.906][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.907][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:55:47.908][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:47.909][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.910][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-11 18:55:47.911][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:47.912][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.913][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.914][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.915][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:47.916][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.917][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.918][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:47.919][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.920][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.921][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.922][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.922][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:47.923][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:47.924][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.925][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.926][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-11 18:55:47.928][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.929][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-11 18:55:47.930][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.931][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:47.932][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.933][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.934][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.935][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.936][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-11 18:55:47.937][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:47.938][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.949][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-11 18:55:47.951][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:47.952][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.953][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:47.953][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.954][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:47.955][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.956][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.957][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:47.958][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:47.959][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:47.960][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:47.961][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.962][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:47.963][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:47.964][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:47.965][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:47.966][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:55:47.967][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.968][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.969][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.970][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.970][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.971][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.972][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.973][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.974][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.975][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.976][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.977][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.977][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.978][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.979][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.980][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.981][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.982][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.983][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.984][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.985][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.986][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.987][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.988][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.989][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.990][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:47.991][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.992][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.993][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.994][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[2023-04-11 18:55:47.995][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:47.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:47.997][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:47.998][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:47.999][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.000][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.000][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.001][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.002][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.003][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.004][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.005][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.006][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.007][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.007][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.012][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.014][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.015][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.016][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[2023-04-11 18:55:48.017][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.018][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.019][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.020][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.021][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.022][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.023][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.024][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.025][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.026][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.027][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.028][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.029][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.030][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.030][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.031][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.032][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.034][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.035][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.036][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.037][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.037][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.038][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.039][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.040][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.041][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.043][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.044][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-11 18:55:48.045][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-11 18:55:48.046][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-11 18:55:48.048][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-11 18:55:48.049][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-11 18:55:48.051][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-11 18:55:48.052][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-11 18:55:48.053][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-11 18:55:48.055][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-11 18:55:48.056][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-11 18:55:48.057][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-11 18:55:48.059][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-11 18:55:48.060][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-11 18:55:48.062][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-11 18:55:48.063][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-11 18:55:48.064][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:55:48.066][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-11 18:55:48.067][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-11 18:55:48.069][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-11 18:55:48.070][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-11 18:55:48.072][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-11 18:55:48.073][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-11 18:55:48.075][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-11 18:55:48.076][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-11 18:55:48.078][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-11 18:55:48.079][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-11 18:55:48.080][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-11 18:55:48.082][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-11 18:55:48.083][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-11 18:55:48.098][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-11 18:55:48.101][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-11 18:55:48.103][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-11 18:55:48.104][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-11 18:55:48.106][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-11 18:55:48.107][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-11 18:55:48.109][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-11 18:55:48.110][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-11 18:55:48.111][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-11 18:55:48.113][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-11 18:55:48.114][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-11 18:55:48.116][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-11 18:55:48.117][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-11 18:55:48.119][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-11 18:55:48.120][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-11 18:55:48.121][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-11 18:55:48.123][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-11 18:55:48.124][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-11 18:55:48.126][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-11 18:55:48.127][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-11 18:55:48.128][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-11 18:55:48.130][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-11 18:55:48.131][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-11 18:55:48.132][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-11 18:55:48.134][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-11 18:55:48.135][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-11 18:55:48.136][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-11 18:55:48.138][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-11 18:55:48.139][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-11 18:55:48.141][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-11 18:55:48.142][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-11 18:55:48.143][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-11 18:55:48.145][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-11 18:55:48.146][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-11 18:55:48.147][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-11 18:55:48.149][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-11 18:55:48.150][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-11 18:55:48.151][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-11 18:55:48.153][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-11 18:55:48.154][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-11 18:55:48.155][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-11 18:55:48.157][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-11 18:55:48.158][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-11 18:55:48.160][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-11 18:55:48.161][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-11 18:55:48.162][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-11 18:55:48.164][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-11 18:55:48.165][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-11 18:55:48.167][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-11 18:55:48.168][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-11 18:55:48.169][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-11 18:55:48.171][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-11 18:55:48.172][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-11 18:55:48.173][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-11 18:55:48.175][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-11 18:55:48.176][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-11 18:55:48.177][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-11 18:55:48.178][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.179][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.180][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.181][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[2023-04-11 18:55:48.182][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.183][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.184][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.186][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.187][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.188][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.189][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.190][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.191][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.192][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.193][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.194][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.200][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.201][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.202][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.203][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.205][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.207][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.219][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.220][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.221][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.223][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.224][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.225][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.226][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.227][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.234][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[2023-04-11 18:55:48.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.251][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.252][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.253][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.254][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.255][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.256][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.257][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.257][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.259][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.260][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.261][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.262][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.263][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.264][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.265][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.266][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.267][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.268][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.270][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.271][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.272][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.274][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.275][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.276][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.277][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.277][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[2023-04-11 18:55:48.278][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.280][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.282][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.283][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.283][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.284][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.285][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.286][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.288][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.289][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.290][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.291][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.292][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.294][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.296][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:48.296][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-11 18:55:48.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:48.298][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:48.299][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:48.300][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:48.301][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:48.302][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[2023-04-11 18:55:48.303][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-11 18:55:48.304][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:55:48.306][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:48.307][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-11 18:55:48.308][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:48.309][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-11 18:55:48.310][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:48.311][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-11 18:55:48.312][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:48.313][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-11 18:55:48.314][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-11 18:55:48.315][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-11 18:55:48.316][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:48.317][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-11 18:55:48.318][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-11 18:55:48.319][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-11 18:55:48.320][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-11 18:55:48.321][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-11 18:55:48.321][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-11 18:55:48.322][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-11 18:55:48.323][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:48.324][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:48.325][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-11 18:55:48.326][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-11 18:55:48.326][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-11 18:55:48.327][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-11 18:55:48.328][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:55:48.328][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-11 18:55:48.329][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-11 18:55:48.330][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-11 18:55:48.331][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-11 18:55:48.332][self$setPropertyValue]
biodb.DEBUG[2023-04-11 18:55:48.333][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-11 18:55:48.335][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-11 18:55:48.338][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:55:48.339][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-11 18:55:48.340][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-11 18:55:48.341][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-11 18:55:48.343][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-11 18:55:48.344][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-11 18:55:48.345][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-11 18:55:48.346][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-11 18:55:48.347][biodb::testThat]
biodb.INFO [2023-04-11 18:55:48.348][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2023-04-11 18:55:48.349][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-11 18:55:48.350][biodb::testThat]
biodb.DEBUG[2023-04-11 18:55:48.354][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[2023-04-11 18:55:48.359][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-11 18:55:48.360][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-04-11 18:55:48.361][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-11 18:55:48.406][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-04-11 18:55:49.289][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-04-11 18:55:49.290][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-11 18:55:49.292][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-04-11 18:55:49.293][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2023-04-11 18:55:49.295][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-04-11 18:55:49.296][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-11 18:55:49.297][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-11 18:55:49.298][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-11 18:55:49.299][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-11 18:55:49.302][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:49.303][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:49.304][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:49.310][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:49.311][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:49.312][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:49.313][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-11 18:55:49.314][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2023-04-11 18:55:49.317][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-11 18:55:49.318][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-11 18:55:49.319][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2023-04-11 18:55:50.034][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2023-04-11 18:55:50.759][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-11 18:55:50.767][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2023-04-11 18:55:50.779][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2023-04-11 18:55:50.791][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2023-04-11 18:55:50.796][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-11 18:55:50.817][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-11 18:55:50.842][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-11 18:55:50.844][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:50.845][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:50.846][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:50.852][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:50.853][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:50.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:50.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:55:50.860][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:50.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:50.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.865][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:50.866][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:50.867][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.868][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:50.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:50.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:50.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:50.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.883][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:50.884][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:50.885][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.886][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.887][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:50.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:50.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.891][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:50.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:50.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.895][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:50.896][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:50.897][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.898][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.902][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:50.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:50.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.907][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:50.908][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:50.909][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.910][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.914][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:55:50.915][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:50.916][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.917][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.918][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:55:50.919][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:50.920][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.921][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.925][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:50.926][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:50.927][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.928][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:50.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:50.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.936][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.937][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.938][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.939][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.941][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.943][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.944][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.948][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:55:50.949][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.950][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.951][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.952][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:55:50.953][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.954][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.955][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.956][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.960][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.963][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.964][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:55:50.965][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.966][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.967][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.971][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.975][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.976][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.977][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.978][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:50.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:50.983][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:50.997][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:50.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.002][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.003][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.004][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.005][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.010][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.012][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.013][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.014][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.018][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.021][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.022][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.024][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.026][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.028][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.030][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.031][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.032][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.033][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.034][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.035][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.036][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.037][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:55:51.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:51.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:51.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:51.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:51.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:51.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:51.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:55:51.056][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.060][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.067][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.068][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.069][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.070][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.071][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.072][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.073][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.074][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.078][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:51.079][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-11 18:55:51.080][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.081][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.082][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:51.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-11 18:55:51.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.087][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.099][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.100][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.101][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.102][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.103][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.105][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.106][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.111][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:55:51.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.113][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.114][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.115][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-11 18:55:51.116][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.117][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.118][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.123][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.127][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.135][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.139][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.154][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.157][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.161][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:55:51.162][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.163][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.164][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.165][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-11 18:55:51.166][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.167][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.168][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.169][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.170][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.172][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.173][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.174][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.175][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.176][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.177][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.178][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-11 18:55:51.179][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.180][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.181][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.186][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.187][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.188][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.189][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.190][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.191][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.192][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.193][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.194][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.195][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.196][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.197][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.198][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.199][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.200][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.201][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.202][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.203][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.204][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.205][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.206][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.207][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.208][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.209][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.210][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.211][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.212][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.213][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.217][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.221][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.222][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.223][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.224][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.225][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.226][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.227][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.228][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.229][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.230][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.231][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.232][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.233][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.234][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.235][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.236][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.237][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.238][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.239][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.240][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-11 18:55:51.241][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-04-11 18:55:51.243][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-11 18:55:51.245][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:51.245][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:51.246][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:51.252][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:51.253][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:51.253][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:51.254][FUN] Functions in observer BiodbConfig: [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[2023-04-11 18:55:51.256][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.259][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.261][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.265][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:55:51.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:55:51.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.268][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.269][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:55:51.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:55:51.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.272][private$selectFields] Fields none
biodb.TRACE[2023-04-11 18:55:51.273][private$selectFields]
biodb.TRACE[2023-04-11 18:55:51.274][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-11 18:55:51.275][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:55:51.276][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:55:51.277][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.278][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.279][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.280][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.281][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.282][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.283][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.284][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.285][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.286][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.287][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.288][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.289][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.301][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.302][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.303][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.304][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.306][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.306][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.307][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.308][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.309][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.310][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.311][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.312][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.313][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.314][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.315][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.316][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.317][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.318][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.319][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.320][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.321][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.322][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.323][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.324][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.325][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.326][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.326][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.327][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.328][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.329][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.330][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.331][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.332][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.333][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.334][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.335][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.336][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.337][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.338][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.339][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.340][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.341][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.342][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.342][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.343][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.344][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.345][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.346][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.347][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.348][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.349][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.350][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:55:51.351][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:55:51.352][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.353][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.354][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.355][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.356][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.357][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.358][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.359][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.360][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.361][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.363][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.364][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.365][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.366][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.367][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.368][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.369][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.370][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.371][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.371][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.372][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.373][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.374][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.375][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.376][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.377][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.378][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.379][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.380][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.381][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.382][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.383][private$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[2023-04-11 18:55:51.384][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.385][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.386][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.387][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.388][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.389][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.390][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.391][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.392][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.393][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.394][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.395][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.396][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.397][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.398][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.399][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.400][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.401][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.402][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.403][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.404][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.405][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.406][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.407][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.408][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.409][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.410][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.411][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.412][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.416][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.420][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.424][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.425][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.426][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.427][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.428][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.429][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.443][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.445][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.446][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.447][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.449][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.449][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.451][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.452][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.453][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.454][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.455][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.456][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.457][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.457][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.459][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.460][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.461][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.462][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.463][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.464][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.465][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.466][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.467][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.469][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.469][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.471][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.472][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.473][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.474][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.475][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.476][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.476][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.477][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.478][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.480][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.481][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.483][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.484][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.485][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.486][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.486][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.488][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.488][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.489][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.490][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.501][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-04-11 18:55:51.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-11 18:55:51.503][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:51.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:51.509][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:51.510][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:51.511][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:51.512][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-11 18:55:51.514][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.518][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-11 18:55:51.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.522][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-11 18:55:51.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-11 18:55:51.524][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.525][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.526][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-11 18:55:51.527][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-11 18:55:51.528][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.529][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.530][private$selectFields] Fields none
biodb.TRACE[2023-04-11 18:55:51.531][private$selectFields]
biodb.TRACE[2023-04-11 18:55:51.532][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-11 18:55:51.533][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-11 18:55:51.534][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:55:51.535][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.536][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.537][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.537][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.538][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.539][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.540][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.541][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.542][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.543][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.544][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.545][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.546][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.547][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.548][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.549][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.550][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.551][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.552][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.553][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.554][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.555][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.556][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.556][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.557][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.558][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.559][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.560][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.561][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.562][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.563][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.564][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.565][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.566][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.567][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.568][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.569][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.570][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.571][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.572][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.573][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.574][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.587][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.589][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.590][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.591][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.592][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.593][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.594][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.595][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.596][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.597][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.598][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.599][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.599][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.600][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.601][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.602][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.603][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.604][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.605][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.606][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.607][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.608][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.609][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:55:51.610][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-11 18:55:51.611][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.612][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.614][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.616][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.617][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.618][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.618][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.619][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.620][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.621][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.622][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.623][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.624][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.625][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.626][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.627][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.628][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.629][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.630][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.631][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.632][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.633][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.634][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.635][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.636][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.637][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.638][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.639][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.640][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.641][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.642][ef$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.643][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-04-11 18:55:51.644][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.645][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.646][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.647][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.648][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.649][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.650][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.651][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.652][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-11 18:55:51.653][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-11 18:55:51.654][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.655][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.656][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.657][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.658][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.659][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.660][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.664][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-11 18:55:51.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.668][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.672][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.676][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-11 18:55:51.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.679][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.680][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.681][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.682][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.683][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.684][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.685][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.686][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.687][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.688][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.689][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-11 18:55:51.690][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.691][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.692][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.693][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.694][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.695][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.696][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.697][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.698][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.699][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.700][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.701][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-11 18:55:51.702][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.703][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.705][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.706][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.707][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.707][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.708][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.710][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.711][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.711][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.713][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-11 18:55:51.714][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-11 18:55:51.715][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.715][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.717][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.731][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.732][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.733][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.735][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.736][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.737][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.738][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.739][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-11 18:55:51.740][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-11 18:55:51.741][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.742][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.743][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.744][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.745][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.746][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.747][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.748][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.749][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.750][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.751][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.752][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-11 18:55:51.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-11 18:55:51.754][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-11 18:55:51.759][private$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[2023-04-11 18:55:51.760][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-11 18:55:51.761][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-04-11 18:55:51.765][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-11 18:55:51.766][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-11 18:55:51.767][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-11 18:55:51.768][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-11 18:55:51.769][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-11 18:55:51.770][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-11 18:55:51.771][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-11 18:55:51.772][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-11 18:55:51.773][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-11 18:55:51.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 169 ]
>
> proc.time()
user system elapsed
27.407 2.254 140.082
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 0.632 | 0.071 | 0.705 | |
| LipidmapsStructureEntry | 0.190 | 0.000 | 0.191 | |