| Back to Multiple platform build/check report for BioC 3.17 |
|
This page was generated on 2023-04-12 10:55:34 -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: 2023-04-12 04:58:08 -0400 (Wed, 12 Apr 2023) |
| EndedAt: 2023-04-12 05:01:47 -0400 (Wed, 12 Apr 2023) |
| EllapsedTime: 218.6 seconds |
| RetCode: 0 |
| Status: OK |
| CheckDir: biodbLipidmaps.Rcheck |
| Warnings: 0 |
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.17-bioc/R/bin/R CMD check --install=check:biodbLipidmaps.install-out.txt --library=/home/biocbuild/bbs-3.17-bioc/R/site-library --timings biodbLipidmaps_1.5.0.tar.gz
###
##############################################################################
##############################################################################
* using log directory ‘/home/biocbuild/bbs-3.17-bioc/meat/biodbLipidmaps.Rcheck’
* using R Under development (unstable) (2023-02-14 r83833)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was compiled by
gcc (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0
* running under: Ubuntu 20.04.6 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 Under development (unstable) (2023-02-14 r83833) -- "Unsuffered Consequences"
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 [2023-04-12 04:58:52.692][biodb::testContext]
biodb.INFO [2023-04-12 04:58:52.695][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:52.696][biodb::testContext] Test context - Generic tests
biodb.INFO [2023-04-12 04:58:52.697][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 04:58:52.698][biodb::testContext]
biodb.INFO [2023-04-12 04:58:52.715][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:52.717][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:52.725][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:52.726][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 04:58:52.727][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 04:58:52.728][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.729][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.730][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.731][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 04:58:52.750][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 04:58:52.751][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.752][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.753][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.754][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 04:58:52.755][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 04:58:52.756][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.757][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.758][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.759][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 04:58:52.760][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 04:58:52.761][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 04:58:52.762][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.763][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.764][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[2023-04-12 04:58:52.765][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 04:58:52.766][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 04:58:52.767][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 04:58:52.768][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.769][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.770][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.771][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 04:58:52.772][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 04:58:52.772][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.773][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.774][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.775][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 04:58:52.776][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 04:58:52.777][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 04:58:52.778][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.779][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.780][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.781][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 04:58:52.782][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 04:58:52.783][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.784][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.785][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.786][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 04:58:52.787][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 04:58:52.788][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 04:58:52.789][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.789][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.790][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.791][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:52.792][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 04:58:52.793][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 04:58:52.794][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 04:58:52.795][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 04:58:52.796][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 04:58:52.797][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.798][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.799][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.800][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 04:58:52.801][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 04:58:52.802][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.803][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.804][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.805][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 04:58:52.806][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 04:58:52.807][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.808][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.809][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.810][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 04:58:52.811][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 04:58:52.811][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.812][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.813][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.814][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 04:58:52.815][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 04:58:52.816][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.817][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.818][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.819][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 04:58:52.820][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 04:58:52.821][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.822][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.823][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.824][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 04:58:52.825][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 04:58:52.830][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 04:58:52.831][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.832][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.832][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[2023-04-12 04:58:52.833][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 04:58:52.834][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 04:58:52.836][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 04:58:52.836][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:52.837][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:52.838][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:52.847][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 04:58:52.884][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.922][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 04:58:52.923][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.924][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:52.925][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.926][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.928][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.929][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.930][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:52.931][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:52.932][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.933][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 04:58:52.934][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:52.935][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.936][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.937][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:52.937][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:52.937][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:52.937][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:52.937][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:52.938][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:52.939][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:52.939][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:52.940][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:52.941][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:52.942][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:52.943][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.944][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.945][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:52.946][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:52.947][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.948][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.949][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 04:58:52.951][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.952][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:52.953][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.954][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:52.955][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.956][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.957][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.958][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.959][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:52.960][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:52.961][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.962][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 04:58:52.963][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:52.964][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.965][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.966][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:52.966][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:52.966][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 04:58:52.966][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 04:58:52.966][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 04:58:52.968][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:52.968][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:52.969][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:52.970][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:52.971][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:52.972][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:52.973][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.974][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.975][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:52.976][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:52.977][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.978][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.979][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 04:58:52.981][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.982][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 04:58:52.983][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.984][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:52.985][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.986][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.987][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.988][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:52.989][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:52.990][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:52.991][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:52.992][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 04:58:52.993][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:52.994][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.995][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:52.996][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:52.997][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:52.998][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:52.999][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:53.000][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:53.001][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:53.002][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:53.002][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.004][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.005][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:53.005][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:53.006][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:53.007][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.009][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 04:58:53.011][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.012][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 04:58:53.013][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.014][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:53.015][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.016][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.017][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:53.018][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.019][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 04:58:53.020][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:53.021][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:53.022][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 04:58:53.022][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:53.023][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.024][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.025][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.026][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:53.027][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:53.028][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:53.029][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:53.030][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:53.031][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:53.032][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.033][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.034][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:53.035][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:53.036][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:53.037][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.042][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:53.042][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.043][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[2023-04-12 04:58:53.044][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.045][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.054][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.055][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.055][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.056][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.057][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.058][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.059][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.060][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.061][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.062][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.063][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.064][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.064][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.065][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.066][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.067][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.068][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.069][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.070][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.071][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.072][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.073][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.073][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.074][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.075][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.076][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.077][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.078][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.079][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.080][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.081][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.082][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.083][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.084][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.084][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.085][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.086][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.087][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.088][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.089][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.090][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.091][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.092][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.093][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.094][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.095][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.096][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.097][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.097][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.098][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.099][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.100][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.101][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.102][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.103][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.104][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.105][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.106][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.107][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.108][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.109][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.110][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.111][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.112][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.113][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.114][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.114][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.115][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.116][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.117][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.118][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.119][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.120][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.121][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.122][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.123][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 04:58:53.128][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 04:58:53.129][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 04:58:53.130][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 04:58:53.132][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 04:58:53.133][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 04:58:53.134][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:53.136][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:53.137][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 04:58:53.138][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 04:58:53.140][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 04:58:53.141][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 04:58:53.143][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 04:58:53.144][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 04:58:53.145][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 04:58:53.147][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:53.148][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 04:58:53.149][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 04:58:53.151][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 04:58:53.152][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 04:58:53.153][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 04:58:53.155][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 04:58:53.156][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 04:58:53.157][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 04:58:53.159][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 04:58:53.160][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 04:58:53.162][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 04:58:53.170][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 04:58:53.172][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 04:58:53.173][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 04:58:53.175][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 04:58:53.176][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 04:58:53.178][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 04:58:53.179][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 04:58:53.180][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 04:58:53.182][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 04:58:53.183][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 04:58:53.185][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 04:58:53.186][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 04:58:53.187][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 04:58:53.189][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 04:58:53.190][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 04:58:53.192][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 04:58:53.193][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 04:58:53.194][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 04:58:53.196][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 04:58:53.197][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 04:58:53.198][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 04:58:53.200][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 04:58:53.201][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 04:58:53.202][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 04:58:53.204][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 04:58:53.205][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 04:58:53.206][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 04:58:53.207][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 04:58:53.209][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 04:58:53.210][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 04:58:53.212][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 04:58:53.214][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 04:58:53.215][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 04:58:53.216][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 04:58:53.218][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 04:58:53.219][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 04:58:53.220][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 04:58:53.221][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 04:58:53.223][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 04:58:53.224][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 04:58:53.225][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 04:58:53.227][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 04:58:53.228][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 04:58:53.230][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 04:58:53.231][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 04:58:53.232][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 04:58:53.234][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 04:58:53.235][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 04:58:53.236][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 04:58:53.238][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 04:58:53.239][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 04:58:53.240][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 04:58:53.242][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 04:58:53.243][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 04:58:53.244][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 04:58:53.246][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 04:58:53.252][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 04:58:53.253][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 04:58:53.257][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 04:58:53.258][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.260][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.267][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.268][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.270][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.271][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.272][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.272][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.273][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.274][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.275][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.277][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.279][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.280][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.281][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.281][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.283][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.285][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.286][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.287][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.288][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.289][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.290][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.290][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.291][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.292][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.293][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.294][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.295][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.297][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.299][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.300][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.301][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.302][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.303][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.304][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.305][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[2023-04-12 04:58:53.306][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.306][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.307][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.308][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.309][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.310][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.310][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.311][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.312][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.313][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.314][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.315][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.315][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.316][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.317][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.318][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.319][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.320][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.320][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.321][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.322][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.323][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.324][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.325][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.325][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.326][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.327][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.328][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.329][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.330][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.330][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.331][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.332][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.333][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.334][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[2023-04-12 04:58:53.335][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.336][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.336][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.337][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.338][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.339][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.340][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[2023-04-12 04:58:53.341][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.341][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.342][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.343][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.344][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.345][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.345][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.346][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.347][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.348][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.349][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.349][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.350][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.351][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.352][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.353][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.353][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.354][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.355][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.356][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.357][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.357][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.358][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.359][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.360][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.361][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.362][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 04:58:53.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.365][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.366][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.366][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.367][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.368][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:58:53.370][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-12 04:58:53.378][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 04:58:53.380][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:53.381][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.382][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.383][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 04:58:53.384][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.385][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.386][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.387][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.388][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 04:58:53.389][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 04:58:53.390][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.391][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-12 04:58:53.392][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-12 04:58:53.393][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-12 04:58:53.394][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 04:58:53.394][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 04:58:53.394][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 04:58:53.396][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 04:58:53.396][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:53.397][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:53.398][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 04:58:53.399][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 04:58:53.400][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 04:58:53.401][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 04:58:53.402][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 04:58:53.402][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-12 04:58:53.403][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 04:58:53.404][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 04:58:53.410][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 04:58:53.411][self$setPropertyValue]
biodb.DEBUG[2023-04-12 04:58:53.417][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-12 04:58:53.418][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 04:58:53.443][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 04:58:53.444][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-12 04:58:53.449][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 04:58:53.453][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-12 04:58:53.457][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-12 04:58:53.458][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-12 04:58:53.460][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-12 04:58:53.461][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-12 04:58:53.478][biodb::testThat]
biodb.INFO [2023-04-12 04:58:53.479][biodb::testThat] Running test function test.entry.fields (" Entry fields have a correct value ").
biodb.INFO [2023-04-12 04:58:53.480][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:53.481][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:53.485][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[2023-04-12 04:58:53.490][biodb$getFactory()$createEntryFromCo ...] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:53.494][biodb$getFactory()$createEntryFromCo ...] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-12 04:58:53.502][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:53.504][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:53.504][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:53.517][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:53.518][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:53.519][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:53.520][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:53.532][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.534][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.535][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.536][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.537][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.549][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.550][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.551][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.555][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.556][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:53.557][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.558][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.559][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:53.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.562][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.563][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:53.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.567][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.594][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.596][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:53.597][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.598][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.602][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.603][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.604][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.605][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.606][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.607][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.608][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.609][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.613][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:58:53.614][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.615][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.616][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.617][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:58:53.618][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:53.619][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.620][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.624][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.628][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.635][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.636][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.637][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.638][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.639][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.640][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.641][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.642][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.646][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:58:53.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.648][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.649][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.650][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 04:58:53.651][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.652][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.653][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.654][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.655][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.656][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.657][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.658][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.659][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.660][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.660][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.662][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:58:53.663][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.663][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.664][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.695][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.696][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.697][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.698][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.699][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.700][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.701][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.702][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.733][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.735][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.736][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.737][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.738][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.739][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.740][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.741][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.742][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.743][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.744][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.745][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.749][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.751][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.752][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.753][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.754][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.755][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.756][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.757][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.758][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.759][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.760][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.761][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.763][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.764][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.765][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.769][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.773][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.780][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.781][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.782][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.783][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.784][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.785][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.786][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.786][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.787][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.788][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.789][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.790][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:53.791][biodb$getFactory()$createEntryFromCo ...] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-12 04:58:53.797][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:53.798][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:53.799][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.800][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.801][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:53.802][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:53.803][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.804][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:53.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:53.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.808][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:53.809][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:53.810][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.811][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.826][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.827][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.828][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.829][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.842][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.844][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.845][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.846][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.851][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.852][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.853][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.854][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.855][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.856][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.857][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.858][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.860][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.861][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.862][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.868][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.869][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.870][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.871][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.872][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.876][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.880][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.881][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.882][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.883][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.884][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.890][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:53.892][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.893][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.901][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.903][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.904][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.905][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.906][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.907][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.908][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.909][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.909][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.913][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.914][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.915][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.916][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.917][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:53.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:53.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.929][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.933][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.934][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.935][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.936][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.937][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.941][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.942][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.943][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.944][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.945][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:53.946][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:53.947][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.947][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.955][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.958][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.959][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.963][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.967][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.968][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.969][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.970][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.971][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.972][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:53.973][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.974][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.981][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.983][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.984][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.985][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.986][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.987][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.988][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.989][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.990][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.991][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.992][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.994][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.995][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.995][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:53.996][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:53.997][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:53.998][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:53.999][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.000][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.008][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.009][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.010][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.012][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.016][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.018][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.018][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.019][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.021][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.022][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.023][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.024][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.025][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.036][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.037][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.038][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.040][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.041][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.042][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.043][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.044][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.048][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.049][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.050][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.051][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.053][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.054][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.055][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.056][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.064][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.066][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.067][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.068][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.073][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:54.074][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:54.075][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.076][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.081][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:54.083][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:54.084][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.085][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.090][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.092][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.093][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.094][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.099][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.100][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.101][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.102][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.107][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.145][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.146][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.147][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:54.153][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.154][biodb::testThat] Running test function test.rt.unit (" RT unit is defined when there is an RT value. ").
biodb.INFO [2023-04-12 04:58:54.155][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.156][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:54.169][private$loadEntries] Creating entries from ids [1]: "LMFA00000001".
biodb.DEBUG[2023-04-12 04:58:54.178][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:58:54.181][cch$loadFileContent] Trying to load 1 files from cache: [1]: "LMFA00000001".
biodb.TRACE[2023-04-12 04:58:54.183][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:54.184][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv".
biodb.DEBUG[2023-04-12 04:58:54.185][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:58:54.230][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-12 04:58:54.231][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-12 04:58:54.233][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:58:54.234][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:58:54.235][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:58:54.240][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:58:54.241][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:58:54.242][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:58:54.243][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:58:54.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.249][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.258][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.259][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.260][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.261][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.262][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.263][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:58:54.264][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.265][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.269][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:54.270][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:58:54.271][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.272][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.273][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:54.274][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:58:54.275][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.276][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.277][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.281][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:58:54.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.288][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:54.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:54.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.292][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:54.293][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:58:54.294][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.295][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.299][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:58:54.300][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.301][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.302][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.303][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:58:54.304][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:54.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.309][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:54.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:54.311][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.312][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.313][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:58:54.314][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:58:54.315][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.316][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.320][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.321][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.324][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.326][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.327][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.328][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.332][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:58:54.333][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.334][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.334][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.336][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 04:58:54.337][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.337][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.338][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.339][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.340][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.341][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.342][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.343][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.344][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.345][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.346][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.347][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:58:54.348][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.349][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.350][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.354][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.355][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.356][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.363][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.364][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.365][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.366][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.367][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.368][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.369][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.370][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.370][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.371][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.375][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.382][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:54.383][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:54.384][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.385][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.386][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:54.387][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:54.388][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.389][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.390][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.391][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.392][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.393][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.394][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:54.395][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:58:54.396][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.396][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.397][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.398][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.399][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.400][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.401][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.402][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.403][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.404][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.405][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.406][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.407][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.408][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.412][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.416][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.417][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.418][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.419][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.420][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:58:54.421][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:58:54.422][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.423][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.424][self$createEntryFromContent] Accession numbers: LMFA00000001.
biodb.TRACE[2023-04-12 04:58:54.425][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.
biodb.TRACE[2023-04-12 04:58:54.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.
biodb.TRACE[2023-04-12 04:58:54.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.429][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.min.
biodb.TRACE[2023-04-12 04:58:54.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.min.
biodb.TRACE[2023-04-12 04:58:54.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.432][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.432][self$getBiodb()$getEntryFields()$get] Asked field names are: chrom.rt.max.
biodb.TRACE[2023-04-12 04:58:54.433][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chrom.rt.max.
biodb.TRACE[2023-04-12 04:58:54.434][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.435][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:54.442][biodb::testThat]
biodb.INFO [2023-04-12 04:58:54.443][biodb::testThat] Running test function test.searchForEntries (" We can search for an entry by searchable field ").
biodb.INFO [2023-04-12 04:58:54.444][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:54.445][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:54.449][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.450][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.451][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.452][ef$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.453][function(conn, opt)] Testing searchForEntries() with entry "LMFA00000001" and field "name".
biodb.TRACE[2023-04-12 04:58:54.480][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.482][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.483][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.484][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.485][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.486][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.487][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:54.488][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:54.489][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:54.490][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:54.491][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:54.494][function(conn, opt)] With value "2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-12 04:58:54.507][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[2023-04-12 04:58:54.527][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:54.528][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:54.530][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride".
biodb.TRACE[2023-04-12 04:58:55.856][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride).
biodb.DEBUG[2023-04-12 04:58:56.555][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:58:56.563][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content"
biodb.TRACE[2023-04-12 04:58:56.589][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.request"
biodb.DEBUG[2023-04-12 04:58:56.595][function(conn, opt)] With found IDs [1]: "LMFA00000001".
biodb.TRACE[2023-04-12 04:58:56.610][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:56.612][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:56.613][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.614][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:56.616][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.617][biodb::testThat] Running test function test.searchByName (" We can search for an entry by name. ").
biodb.INFO [2023-04-12 04:58:56.618][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:56.619][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:56.667][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:56.669][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:56.670][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.671][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.672][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:56.673][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:56.674][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.675][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:56.676][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:56.677][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:56.678][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:56.690][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:56.881][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-12 04:58:56.888][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:56.956][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-12 04:58:56.959][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:56.961][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.INFO [2023-04-12 04:58:56.983][biodb::testThat]
biodb.INFO [2023-04-12 04:58:56.984][biodb::testThat] Running test function testEntryLoading (" We can load an entry from the database. ").
biodb.INFO [2023-04-12 04:58:56.985][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:56.986][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:57.014][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.015][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.016][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.017][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.018][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.019][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.020][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.021][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.022][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:57.023][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:57.024][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.025][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.026][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:57.027][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:57.028][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.029][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.072][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.074][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.075][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.076][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.077][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.078][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 04:58:57.079][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.080][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.081][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:57.082][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 04:58:57.082][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.083][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:57.084][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:57.085][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 04:58:57.086][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:57.087][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:57.091][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.092][biodb::testThat] Running test function test.entry.page.url (" We can get a URL pointing to the entry page. ").
biodb.INFO [2023-04-12 04:58:57.093][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:57.094][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.100][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.101][biodb::testThat] Running test function test.entry.image.url (" We can get a URL pointing to the entry image. ").
biodb.INFO [2023-04-12 04:58:57.102][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:57.103][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.109][biodb::testThat]
biodb.INFO [2023-04-12 04:58:57.110][biodb::testThat] Running test function test.entry.page.url.download (" The entry page URL can be downloaded. ").
biodb.INFO [2023-04-12 04:58:57.111][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:57.112][biodb::testThat]
biodb.DEBUG[2023-04-12 04:58:57.116][function(conn, opt)] Trying to download "https://www.lipidmaps.org/data?LMID=LMFA00000001".
biodb.DEBUG[2023-04-12 04:58:57.981][getUrlContent] Use RCurl for downloading content of URL https://www.lipidmaps.org/data?LMID=LMFA00000001.
biodb.INFO [2023-04-12 04:58:58.454][biodb::testThat]
biodb.INFO [2023-04-12 04:58:58.456][biodb::testThat] Running test function test.entry.image.url.download (" The entry image URL can be downloaded. ").
biodb.INFO [2023-04-12 04:58:58.458][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:58.459][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:58.474][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.476][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.478][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.479][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.481][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.483][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.484][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.485][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 04:58:58.488][biodb::testThat]
biodb.INFO [2023-04-12 04:58:58.490][biodb::testThat] Running test function test.searchCompound (" We can search for a compound ").
biodb.INFO [2023-04-12 04:58:58.491][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:58:58.493][biodb::testThat]
biodb.TRACE[2023-04-12 04:58:58.521][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.523][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.525][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.526][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.528][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.530][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.531][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.534][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:58:58.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:58:58.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:58.636][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-12 04:58:58.639][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:58.641][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-12 04:58:58.642][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:58.643][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.DEBUG[2023-04-12 04:58:58.732][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride".
biodb.DEBUG[2023-04-12 04:58:58.736][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:58:58.737][cch$loadFileContent] Trying to load 1 files from cache: [1]: "e8702bf6dc5a5afd048f747914fd7a6a".
biodb.TRACE[2023-04-12 04:58:58.739][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:58:58.740][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/e8702bf6dc5a5afd048f747914fd7a6a.content".
biodb.TRACE[2023-04-12 04:58:58.756][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:58:58.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.771][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:58:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.788][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.789][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.790][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.791][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.792][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.793][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.794][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.795][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.796][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.800][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:58:58.804][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:58:58.805][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:58:58.806][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:58:58.845][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-04-12 04:58:58.871][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:58:58.872][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:58:58.889][private$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[2023-04-12 04:59:03.363][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[2023-04-12 04:59:15.059][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.INFO [2023-04-12 04:59:15.082][self$getFolderPath] Create cache folder "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b" for "lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b".
biodb.TRACE[2023-04-12 04:59:15.091][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.content"
biodb.TRACE[2023-04-12 04:59:15.128][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/304383a7dc8c451be84009e31d831359.request"
biodb.DEBUG[2023-04-12 04:59:16.224][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride&ExactMass=626.491025&ExactMassOffSet=1e-06".
biodb.DEBUG[2023-04-12 04:59:16.229][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:16.231][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:16.233][private$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[2023-04-12 04:59:16.974][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[2023-04-12 04:59:17.681][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:17.695][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.content"
biodb.TRACE[2023-04-12 04:59:17.719][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/7f71825f1888a7b29e4b8407502d21e3.request"
biodb.DEBUG[2023-04-12 04:59:17.830][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[2023-04-12 04:59:17.834][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:17.835][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:17.838][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06".
biodb.TRACE[2023-04-12 04:59:18.501][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=2-methoxy-12-methyloctadec-17-en-5-ynoyl%20anhydride&ExactMass=626.491026&ExactMassOffSet=2e-06).
biodb.DEBUG[2023-04-12 04:59:19.516][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:19.523][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.content"
biodb.TRACE[2023-04-12 04:59:19.535][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/fd41c675dd237f33cdaafcbb15058c54.request"
biodb.TRACE[2023-04-12 04:59:19.556][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:19.557][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:19.558][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.559][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:19.573][biodb::testThat]
biodb.INFO [2023-04-12 04:59:19.574][biodb::testThat] Running test function test_annotateMzValues_input_vector (" annotateMzValues() accepts a single vector. ").
biodb.INFO [2023-04-12 04:59:19.575][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:19.576][biodb::testThat]
biodb.TRACE[2023-04-12 04:59:19.619][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:59:19.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:59:19.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:19.624][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:19.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:19.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:19.629][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:19.633][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.634][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.635][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.636][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:19.637][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.638][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.639][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.640][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:19.641][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.642][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:19.643][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:19.644][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:19.657][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:19.658][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:19.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:19.665][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:19.666][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:19.667][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:19.668][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:19.709][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.01".
biodb.DEBUG[2023-04-12 04:59:19.713][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:19.714][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:19.716][private$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[2023-04-12 04:59:23.946][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[2023-04-12 04:59:35.253][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:35.265][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content"
biodb.TRACE[2023-04-12 04:59:35.291][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.request"
biodb.DEBUG[2023-04-12 04:59:36.215][private$loadEntries] Creating entries from ids [2]: "LMFA00000002, LMFA00000003".
biodb.DEBUG[2023-04-12 04:59:36.261][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-12 04:59:36.263][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000002, LMFA00000003".
biodb.TRACE[2023-04-12 04:59:36.265][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-12 04:59:36.266][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:36.267][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:36.268][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 04:59:36.269][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:36.270][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:36.287][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:36.288][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:36.289][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:36.295][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:36.296][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:36.297][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:36.298][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:36.300][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.DEBUG[2023-04-12 04:59:36.303][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:36.304][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:36.305][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv".
biodb.TRACE[2023-04-12 04:59:37.624][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000002?format=tsv).
biodb.DEBUG[2023-04-12 04:59:38.322][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:38.330][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.content"
biodb.TRACE[2023-04-12 04:59:38.342][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/a989db4a318873c598872a885a94e78c.request"
biodb.DEBUG[2023-04-12 04:59:38.347][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:38.348][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:38.349][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:38.355][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:38.356][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:38.357][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:38.358][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:38.359][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.DEBUG[2023-04-12 04:59:38.362][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:38.363][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:38.364][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv".
biodb.TRACE[2023-04-12 04:59:39.038][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000003?format=tsv).
biodb.DEBUG[2023-04-12 04:59:39.702][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:39.711][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.content"
biodb.TRACE[2023-04-12 04:59:39.723][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f88961343869f5da5bc09cbcc0e6185e.request"
biodb.TRACE[2023-04-12 04:59:39.734][private$doSaveContentToFile] Saving to cache [2]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv, /home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000003.tsv"
biodb.DEBUG[2023-04-12 04:59:39.739][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 04:59:39.760][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-12 04:59:39.762][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-12 04:59:39.763][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:39.764][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:39.765][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:39.771][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:39.806][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:39.807][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:39.808][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.TRACE[2023-04-12 04:59:39.814][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:39.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:39.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.819][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:39.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:39.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.828][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:39.829][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:39.830][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.831][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.832][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:39.833][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:39.834][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.835][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.840][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:59:39.842][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:59:39.843][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.844][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.845][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:39.846][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:39.847][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.848][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.849][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:39.851][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:39.852][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.852][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.854][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:39.855][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:39.856][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.857][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.861][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:39.862][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:39.863][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.864][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.866][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:39.867][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:39.868][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.869][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.874][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:59:39.875][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:39.876][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.877][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.878][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:59:39.880][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:39.881][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.882][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.886][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:39.888][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:39.889][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.890][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.891][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:39.892][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:39.893][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.894][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.899][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:39.900][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.901][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.902][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.904][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:39.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.911][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:59:39.912][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.913][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.914][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.915][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 04:59:39.916][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.918][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.919][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.920][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:39.921][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.922][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.923][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.924][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:39.925][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.926][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.927][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.928][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:59:39.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:39.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.936][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:39.938][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:39.939][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.940][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.941][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:39.942][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:39.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.946][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:39.948][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:39.949][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.951][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:39.952][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:39.953][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.954][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.956][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:39.957][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:39.958][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.959][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.960][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:39.961][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:39.962][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.964][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:39.965][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:39.966][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:39.967][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:39.968][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:39.992][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:39.993][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:39.994][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.001][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.002][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.003][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.004][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.TRACE[2023-04-12 04:59:40.008][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.010][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.011][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.011][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.012][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.014][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.014][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.015][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.020][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 04:59:40.021][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 04:59:40.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.025][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:59:40.026][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 04:59:40.027][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.028][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.029][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:40.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 04:59:40.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.033][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:40.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:40.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.035][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.037][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:40.038][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 04:59:40.039][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.039][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.044][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:40.045][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:40.046][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.047][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.048][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:40.049][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 04:59:40.050][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.051][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.056][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:59:40.057][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.058][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.059][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.060][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 04:59:40.061][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.062][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.063][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.067][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:40.069][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:40.070][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.071][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.072][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 04:59:40.073][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 04:59:40.074][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.075][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.080][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:40.081][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.083][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.084][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.085][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:40.086][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.087][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.088][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.093][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:59:40.095][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.096][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.097][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.098][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 04:59:40.099][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.100][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.101][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.102][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:40.104][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.104][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.105][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.107][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 04:59:40.108][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.109][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.109][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.111][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 04:59:40.112][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 04:59:40.112][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.113][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.118][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.119][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.120][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.121][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.122][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.124][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.125][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.126][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.127][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.131][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.132][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.133][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.134][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.135][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.139][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.142][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.144][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.160][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.161][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.162][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.167][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.168][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.169][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.170][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.171][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.173][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.176][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.180][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.185][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.186][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.187][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.188][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.189][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 04:59:40.190][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 04:59:40.191][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.192][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:40.194][self$createEntryFromContent] Accession numbers: LMFA00000002, LMFA00000003.
biodb.DEBUG[2023-04-12 04:59:40.205][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:40.207][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.208][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.209][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.214][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.215][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.216][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.217][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:40.218][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.220][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.220][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.222][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.226][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.227][private$selectFields]
biodb.TRACE[2023-04-12 04:59:40.228][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:40.229][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:40.230][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.231][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.232][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.233][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.234][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.235][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.236][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.237][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.237][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.238][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.239][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.240][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.241][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.242][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.243][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.244][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:40.245][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.246][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.247][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.248][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.249][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.250][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.251][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.252][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.253][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.254][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.255][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.256][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.265][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-12 04:59:40.267][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.268][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.269][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.274][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.275][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.276][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.277][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.TRACE[2023-04-12 04:59:40.278][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.279][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.280][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.281][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.282][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.283][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.284][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.285][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.286][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.287][private$selectFields]
biodb.TRACE[2023-04-12 04:59:40.288][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:40.289][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:40.290][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.291][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.292][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.293][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.294][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.295][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.296][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.297][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.298][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.312][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.314][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.315][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.316][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.317][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.318][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.319][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:40.320][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.322][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.322][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.323][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.324][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.328][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.329][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.330][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.331][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.332][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-12 04:59:40.333][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.334][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.335][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.340][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.341][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.342][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.343][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:40.344][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.346][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.347][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.347][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.348][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.350][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.350][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.351][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.352][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.353][private$selectFields]
biodb.TRACE[2023-04-12 04:59:40.354][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:40.355][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:40.356][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.357][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.358][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.359][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.360][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.361][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.362][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.362][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.363][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.364][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.365][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:40.366][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.367][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.368][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.369][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.370][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:40.371][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.372][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.373][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.374][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.375][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.376][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.377][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.378][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.379][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.380][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:40.381][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.382][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.383][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-12 04:59:40.384][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:40.385][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:40.395][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:40.396][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:40.397][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.398][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:40.400][biodb::testThat]
biodb.INFO [2023-04-12 04:59:40.401][biodb::testThat] Running test function test_annotateMzValues_ppm_tol (" ppm tolerance works in annotateMzValues() ").
biodb.INFO [2023-04-12 04:59:40.402][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:40.403][biodb::testThat]
biodb.TRACE[2023-04-12 04:59:40.407][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:59:40.408][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:59:40.409][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.410][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.412][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:40.413][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:40.414][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.415][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.416][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.418][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.419][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.420][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.421][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.422][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.423][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.424][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.425][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.426][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.427][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.428][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:40.429][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.430][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:40.431][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:40.431][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:40.528][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:40.529][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:40.529][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:40.535][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:40.537][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:40.538][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:40.538][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 04:59:40.580][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&ExactMass=626.491025&ExactMassOffSet=0.009397365375".
biodb.DEBUG[2023-04-12 04:59:40.584][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:40.585][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:40.586][private$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[2023-04-12 04:59:44.773][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[2023-04-12 04:59:56.150][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 04:59:56.160][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.content"
biodb.TRACE[2023-04-12 04:59:56.188][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/5652f5994fce967a05a065a71bac3ed6.request"
biodb.DEBUG[2023-04-12 04:59:57.401][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:57.425][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:57.426][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:57.427][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:57.433][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:57.434][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:57.435][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:57.436][FUN] Functions in observer BiodbConfig: [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[2023-04-12 04:59:57.448][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.450][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.451][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.452][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.453][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.454][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.455][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.456][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.477][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.478][private$selectFields]
biodb.TRACE[2023-04-12 04:59:57.480][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:57.481][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:57.482][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.483][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.484][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.485][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.486][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.487][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.488][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.489][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.490][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.491][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.502][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.503][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.505][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.506][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.507][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.508][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:57.509][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.514][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.515][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.516][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.517][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.518][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.519][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.520][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.521][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.522][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-12 04:59:57.523][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:57.524][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:57.525][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:57.531][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:57.532][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:57.533][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:57.534][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:57.535][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.537][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.538][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.539][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.540][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.541][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.542][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.543][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.544][private$selectFields]
biodb.TRACE[2023-04-12 04:59:57.545][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:57.546][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:57.547][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.548][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.549][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.550][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.551][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.552][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.553][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.554][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.555][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.556][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.557][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.558][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.559][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.560][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.561][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.562][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:57.563][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.564][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.565][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.566][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.567][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.568][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.569][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.570][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.571][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.572][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.573][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.574][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.575][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-12 04:59:57.576][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:57.577][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:57.578][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:57.584][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:57.585][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:57.586][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:57.587][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:57.588][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.589][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.590][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.591][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.593][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.594][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.595][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.596][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.597][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.598][private$selectFields]
biodb.TRACE[2023-04-12 04:59:57.599][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:57.600][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:57.601][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.603][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.604][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.605][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.606][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.607][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.609][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.610][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.611][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.612][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.613][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:57.614][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.615][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.616][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.617][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.618][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:57.619][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.625][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.626][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.627][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.628][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.629][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.630][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:57.631][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.632][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.634][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-12 04:59:57.635][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:57.636][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:57.646][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:57.647][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:57.649][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.650][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:57.653][biodb::testThat]
biodb.INFO [2023-04-12 04:59:57.654][biodb::testThat] Running test function test_annotateMzValues_input_dataframe_untouched (" Input data frame is not modified by annotateMzValues() ").
biodb.INFO [2023-04-12 04:59:57.655][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:57.656][biodb::testThat]
biodb.TRACE[2023-04-12 04:59:57.660][self$getBiodb()$getEntryFields()$get] Asked field names are: average.mass.
biodb.TRACE[2023-04-12 04:59:57.661][self$getBiodb()$getEntryFields()$get] Realnames of fields are: average.mass.
biodb.TRACE[2023-04-12 04:59:57.662][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.663][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.664][self$getBiodb()$getEntryFields()$get] Asked field names are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:57.665][self$getBiodb()$getEntryFields()$get] Realnames of fields are: molecular.mass.
biodb.TRACE[2023-04-12 04:59:57.666][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.667][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.668][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.670][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.671][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.672][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.673][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.674][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.675][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.676][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.677][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.678][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.679][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.680][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:57.681][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.683][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 04:59:57.684][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:57.685][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 04:59:57.696][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:57.698][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:57.699][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:57.705][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:57.707][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:57.708][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:57.709][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[2023-04-12 04:59:57.768][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[2023-04-12 04:59:57.772][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 04:59:57.774][cch$loadFileContent] Trying to load 1 files from cache: [1]: "f4acf835cb23946f08f684530aa686a3".
biodb.TRACE[2023-04-12 04:59:57.775][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 04:59:57.834][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f4acf835cb23946f08f684530aa686a3.content".
biodb.DEBUG[2023-04-12 04:59:58.752][private$bdb$entriesToDataframe] 3 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 04:59:58.755][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:58.756][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:58.757][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:58.764][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:58.765][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:58.766][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:58.767][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:58.768][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.769][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.770][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.771][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.772][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.773][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.774][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.775][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.776][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.777][private$selectFields]
biodb.TRACE[2023-04-12 04:59:58.778][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:58.779][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:58.780][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.781][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.782][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.783][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.784][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.785][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.786][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.787][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.788][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.789][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.790][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.791][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.792][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.793][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.794][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.795][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:58.796][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.797][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.798][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.799][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.800][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.801][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.802][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.803][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.804][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.805][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.806][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.807][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.808][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000001].
biodb.DEBUG[2023-04-12 04:59:58.809][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:58.810][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:58.811][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:58.817][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:58.818][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:58.819][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:58.820][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 04:59:58.821][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.822][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.823][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.824][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.825][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.826][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.827][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.828][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.829][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.830][private$selectFields]
biodb.TRACE[2023-04-12 04:59:58.831][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:58.832][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:58.832][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.833][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.834][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.835][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.836][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.837][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.838][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.839][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.840][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.841][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.842][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.843][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.844][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.845][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.846][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.847][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:58.848][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.849][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.850][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.851][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.852][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.853][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.854][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.855][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.856][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.857][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.858][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.859][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.860][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000002].
biodb.DEBUG[2023-04-12 04:59:58.861][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:58.862][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:58.863][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:58.869][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:58.870][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:58.870][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:58.871][FUN] Functions in observer BiodbConfig: [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[2023-04-12 04:59:58.873][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.874][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.875][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.876][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.877][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.878][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.879][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.880][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.881][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.882][private$selectFields]
biodb.TRACE[2023-04-12 04:59:58.883][private$selectFields] Fields is null: FALSE
biodb.TRACE[2023-04-12 04:59:58.884][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 04:59:58.885][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.886][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.887][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.888][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.890][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.891][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.892][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.893][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.893][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.894][private$selectFields] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.895][private$organizeFieldsByGroups] Fields [1]: "lipidmaps.structure.id"
biodb.TRACE[2023-04-12 04:59:58.896][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.897][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.898][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.899][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.900][private$organizeFieldsByGroups] Groups [2]: "lipidmaps.structure.id, list()"
biodb.TRACE[2023-04-12 04:59:58.901][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.902][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.903][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.904][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.905][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.906][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.907][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.908][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.909][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 04:59:58.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 04:59:58.913][private$entriesToListOfDataframes] Entry converted to data frame: [1, 1]: [lipidmaps.structure.id] [LMFA00000003].
biodb.DEBUG[2023-04-12 04:59:58.914][private$entriesToListOfDataframes] Converted 3 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 04:59:58.915][private$bdb$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.TRACE[2023-04-12 04:59:58.937][self$getBiodb()$getEntryFields()$get] Asked field names are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:58.939][self$getBiodb()$getEntryFields()$get] Realnames of fields are: nominal.mass.
biodb.TRACE[2023-04-12 04:59:58.940][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 04:59:58.941][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.INFO [2023-04-12 04:59:58.943][biodb::testThat]
biodb.INFO [2023-04-12 04:59:58.944][biodb::testThat] Running test function test.wrong.entry (" Wrong entry gives NULL ").
biodb.INFO [2023-04-12 04:59:58.945][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 04:59:58.946][biodb::testThat]
biodb.DEBUG[2023-04-12 04:59:58.949][private$loadEntries] Creating entries from ids [1]: "WRONGA".
biodb.DEBUG[2023-04-12 04:59:58.950][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 1 id(s)...
biodb.TRACE[2023-04-12 04:59:58.952][cch$loadFileContent] Trying to load 1 files from cache: [1]: "WRONGA".
biodb.TRACE[2023-04-12 04:59:58.953][cch$loadFileContent] file.exist = [1]: "FALSE".
biodb.TRACE[2023-04-12 04:59:58.955][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 04:59:58.956][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 04:59:58.957][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 04:59:58.959][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 04:59:58.959][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 04:59:58.975][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 04:59:58.976][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 04:59:58.977][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 04:59:58.982][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 04:59:58.984][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 04:59:58.985][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 04:59:58.985][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[2023-04-12 04:59:58.987][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.DEBUG[2023-04-12 04:59:58.990][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 04:59:58.991][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 04:59:58.992][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 04:59:59.702][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 04:59:59.704][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 04:59:59.706][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[2023-04-12 04:59:59.708][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:00.635][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:00.637][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:00.638][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:00.639][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:01.290][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:01.293][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:01.296][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[2023-04-12 05:00:01.298][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:02.223][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:02.228][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:02.229][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:02.230][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:04.811][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:04.813][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:04.815][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[2023-04-12 05:00:04.817][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:05.844][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:05.845][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:05.846][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:05.848][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:06.472][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:06.473][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:06.475][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[2023-04-12 05:00:06.477][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:07.532][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:07.533][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:07.534][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:07.536][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:08.177][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:08.180][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:08.182][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[2023-04-12 05:00:08.184][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:09.214][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:09.216][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:09.217][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:09.219][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:09.847][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:09.849][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:09.852][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:09.855][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:10.756][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:10.758][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:10.759][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:10.760][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:11.403][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:11.405][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:11.407][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[2023-04-12 05:00:11.408][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:12.644][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:12.646][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:12.647][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:12.649][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:13.287][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:13.289][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:13.292][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[2023-04-12 05:00:13.294][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:14.226][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:14.228][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:14.230][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:14.233][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:14.885][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:14.887][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:14.889][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[2023-04-12 05:00:14.891][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:16.124][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.DEBUG[2023-04-12 05:00:16.125][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:16.127][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:16.128][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv".
biodb.TRACE[2023-04-12 05:00:16.765][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:16.767][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:16.769][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[2023-04-12 05:00:16.772][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv).
biodb.INFO [2023-04-12 05:00:19.217][private$doSendRequestLoop] Error when retrieving URL content HTTP error 404 (""). When contacting URL "https://www.lipidmaps.org/databases/lmsd/WRONGA?format=tsv". Retrying connection to server...
biodb.TRACE[2023-04-12 05:00:19.228][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/WRONGA.tsv"
biodb.DEBUG[2023-04-12 05:00:19.233][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 05:00:19.257][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 1 content(s).
biodb.DEBUG[2023-04-12 05:00:19.259][self$createEntryFromContent] Parsing 1 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-12 05:00:19.261][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:00:19.263][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:19.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:19.272][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:19.273][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:19.275][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:19.276][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 05:00:19.278][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:19.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:19.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.283][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:19.285][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:19.286][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.287][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.288][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:19.289][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:19.290][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.291][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.293][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:19.294][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:19.295][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.296][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.297][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:19.299][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:19.300][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.301][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.302][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:19.303][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:19.305][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.306][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.307][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:19.308][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:19.310][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.311][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:19.312][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:19.313][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:19.314][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:19.315][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 05:00:19.316][self$createEntryFromContent] Accession numbers: NA.
biodb.DEBUG[2023-04-12 05:00:19.318][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.INFO [2023-04-12 05:00:19.326][biodb::testThat]
biodb.INFO [2023-04-12 05:00:19.327][biodb::testThat] Running test function test.wrong.entry.among.good.ones (" One wrong entry does not block the retrieval of good ones ").
biodb.INFO [2023-04-12 05:00:19.328][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:00:19.330][biodb::testThat]
biodb.DEBUG[2023-04-12 05:00:19.341][function(conn, opt)] IDS: [4]: "WRONGB, LMFA00000001, LMFA00000002, LMFA08040013"
biodb.DEBUG[2023-04-12 05:00:19.342][private$loadEntries] Creating entries from ids [2]: "WRONGB, LMFA08040013".
biodb.DEBUG[2023-04-12 05:00:19.344][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-12 05:00:19.346][cch$loadFileContent] Trying to load 2 files from cache: [2]: "WRONGB, LMFA08040013".
biodb.TRACE[2023-04-12 05:00:19.347][cch$loadFileContent] file.exist = [2]: "FALSE, FALSE".
biodb.TRACE[2023-04-12 05:00:19.348][loadFileContents] Loaded 0 files from cache: none.
biodb.DEBUG[2023-04-12 05:00:19.350][conn$getEntryContent] 0 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 05:00:19.351][conn$getEntryContent] 2 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 05:00:19.352][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 05:00:19.353][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 05:00:19.359][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:00:19.361][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:19.362][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:19.368][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:19.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:19.370][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:19.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:19.372][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.DEBUG[2023-04-12 05:00:19.377][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:19.378][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:19.380][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:23.146][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:23.148][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:23.150][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:23.151][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:24.823][private$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[2023-04-12 05:00:24.825][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:24.826][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:24.828][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:25.443][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:25.446][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:25.448][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:25.450][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:26.359][private$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[2023-04-12 05:00:26.360][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:26.361][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:26.363][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:26.985][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:26.989][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:26.992][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:26.995][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:27.894][private$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[2023-04-12 05:00:27.896][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:27.897][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:27.898][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:28.512][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:28.514][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:28.515][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:28.517][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:29.427][private$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[2023-04-12 05:00:29.429][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:29.431][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:29.433][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:30.057][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:30.059][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:30.061][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:30.063][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:30.916][private$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[2023-04-12 05:00:30.917][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:30.919][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:30.920][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:31.543][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:31.545][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:31.547][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:31.549][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:32.580][private$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[2023-04-12 05:00:32.582][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:32.584][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:32.587][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:33.232][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:33.235][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:33.237][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:33.240][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:34.141][private$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[2023-04-12 05:00:34.143][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:34.144][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:34.145][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:34.759][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:34.762][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:34.764][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:34.766][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:35.678][private$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[2023-04-12 05:00:35.680][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:35.681][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:35.682][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:36.302][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:36.305][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:36.307][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:36.309][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:37.217][private$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[2023-04-12 05:00:37.218][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:37.219][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:37.221][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv".
biodb.TRACE[2023-04-12 05:00:37.836][doesRCurlRequestUrlExist] According to RCurl, URL https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv does not exist.
biodb.TRACE[2023-04-12 05:00:37.838][getUrlRequestResult] Using base::url() for sending request.
biodb.DEBUG[2023-04-12 05:00:37.840][getUrlRequestResult] URL "https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv" does not exist according to RCurl. That may happen with some protocol misunderstanding. Trying with base::url().
biodb.TRACE[2023-04-12 05:00:37.841][getBaseUrlRequestResult] Using base::url() for sending request (https://www.lipidmaps.org/databases/lmsd/WRONGB?format=tsv).
biodb.INFO [2023-04-12 05:00:38.760][private$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[2023-04-12 05:00:38.762][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:00:38.763][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:38.764][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:38.772][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:38.773][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:38.774][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:38.775][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[2023-04-12 05:00:38.776][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.DEBUG[2023-04-12 05:00:38.780][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:38.781][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:38.783][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv".
biodb.TRACE[2023-04-12 05:00:40.210][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA08040013?format=tsv).
biodb.DEBUG[2023-04-12 05:00:40.947][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:00:40.962][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.content"
biodb.TRACE[2023-04-12 05:00:40.981][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/0fdeb15a49cfc75bfed9dd3f524ffa41.request"
biodb.TRACE[2023-04-12 05:00:40.999][private$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[2023-04-12 05:00:41.007][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 05:00:41.034][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-12 05:00:41.036][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-12 05:00:41.039][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:00:41.040][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:41.041][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:41.048][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:41.049][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:41.050][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:41.051][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 05:00:41.053][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.055][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.056][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.057][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.058][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.059][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.060][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.061][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.062][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.064][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.065][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.066][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 05:00:41.067][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:00:41.068][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:41.069][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:41.075][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:41.076][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:41.077][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:41.078][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 05:00:41.083][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.084][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.085][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.086][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.087][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.090][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.091][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.095][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:00:41.097][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:00:41.098][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.099][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.100][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:00:41.101][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:00:41.102][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.103][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.108][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:00:41.109][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:00:41.110][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.111][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.113][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:00:41.114][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:00:41.115][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.116][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.122][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:00:41.123][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:00:41.124][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.125][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.126][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:00:41.128][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:00:41.129][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.130][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.135][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:00:41.136][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:00:41.137][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.138][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.139][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:00:41.140][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:00:41.141][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.143][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.148][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:00:41.150][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:00:41.151][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.152][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:00:41.155][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:00:41.156][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.163][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 05:00:41.165][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:00:41.166][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.167][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.168][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 05:00:41.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:00:41.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.176][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:00:41.177][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:00:41.178][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.179][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.180][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:00:41.182][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:00:41.183][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.184][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.190][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.192][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.193][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.194][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.195][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.196][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.197][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.198][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.203][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 05:00:41.204][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.205][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.206][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.208][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 05:00:41.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.211][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.212][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.213][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.214][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.215][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.216][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.217][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.218][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.221][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.222][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 05:00:41.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.230][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.234][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.238][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.240][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.241][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.242][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.243][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.248][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:41.249][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:41.250][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.251][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.256][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.258][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.259][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.260][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.261][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.262][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.263][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.264][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.265][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.266][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.267][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.269][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.270][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.271][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:00:41.272][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.273][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.275][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.276][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.277][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.278][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.279][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.280][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.281][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.282][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.283][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.284][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.285][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.286][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.290][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.292][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.293][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.294][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.295][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.297][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.298][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.299][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.300][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.302][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.303][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.304][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.305][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.306][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.307][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.308][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.310][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.312][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.313][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.315][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.319][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:41.323][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:00:41.324][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:00:41.325][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:41.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 05:00:41.328][self$createEntryFromContent] Accession numbers: NA, LMFA08040013.
biodb.DEBUG[2023-04-12 05:00:41.329][self$createEntryFromContent] Found 1 entry/ies without an accession number. Set it/them to NULL.
biodb.DEBUG[2023-04-12 05:00:41.330][function(conn, opt)] Entries: [4]: "NULL, <environment>, <environment>, <environment>"
biodb.INFO [2023-04-12 05:00:41.344][biodb::testThat]
biodb.INFO [2023-04-12 05:00:41.345][biodb::testThat] Running test function test.peak.table (" The peak table is correct. ").
biodb.INFO [2023-04-12 05:00:41.347][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:00:41.348][biodb::testThat]
biodb.INFO [2023-04-12 05:00:41.372][biodb::testThat]
biodb.INFO [2023-04-12 05:00:41.374][biodb::testThat] Running test function test.nb.entries (" Nb entries is positive. ").
biodb.INFO [2023-04-12 05:00:41.375][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:00:41.376][biodb::testThat]
biodb.INFO [2023-04-12 05:00:41.384][biodb::testThat]
biodb.INFO [2023-04-12 05:00:41.385][biodb::testThat] Running test function test.entry.ids (" We can get a list of entry ids. ").
biodb.INFO [2023-04-12 05:00:41.387][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:00:41.388][biodb::testThat]
biodb.DEBUG[2023-04-12 05:00:41.407][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.DEBUG[2023-04-12 05:00:41.412][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:41.413][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:41.415][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV".
biodb.TRACE[2023-04-12 05:00:45.544][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV).
biodb.DEBUG[2023-04-12 05:00:56.910][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:00:56.919][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content"
biodb.TRACE[2023-04-12 05:00:56.943][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.request"
biodb.TRACE[2023-04-12 05:00:58.054][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:00:58.056][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:00:58.057][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:58.058][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:00:58.059][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:00:58.060][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:00:58.061][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:00:58.062][ef$get] fields variable is a list.
biodb.INFO [2023-04-12 05:00:58.064][biodb::testThat]
biodb.INFO [2023-04-12 05:00:58.065][biodb::testThat] Running test function test.annotateMzValues (" annotateMzValues() works correctly. ").
biodb.INFO [2023-04-12 05:00:58.065][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:00:58.066][biodb::testThat]
biodb.ERROR[2023-04-12 05:00:58.082][conn$annotateMzValues] No column named "mz" was found inside data frame.
biodb.ERROR[2023-04-12 05:00:58.099][ef$checkIsDefined] Field(s) "foo" is/are not defined.
biodb.INFO [2023-04-12 05:00:58.109][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 05:00:58.111][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-12 05:00:58.112][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-12 05:00:58.113][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 05:00:58.114][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.115][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.116][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.117][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.118][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.118][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.INFO [2023-04-12 05:00:58.129][biodb::testContext]
biodb.INFO [2023-04-12 05:00:58.130][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 05:00:58.132][biodb::testContext] Test context - Web services tests
biodb.INFO [2023-04-12 05:00:58.132][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 05:00:58.133][biodb::testContext]
biodb.INFO [2023-04-12 05:00:58.138][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 05:00:58.140][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 05:00:58.144][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 05:00:58.145][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 05:00:58.146][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 05:00:58.147][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.148][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.149][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.150][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 05:00:58.151][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 05:00:58.152][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.153][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.154][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.155][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 05:00:58.156][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 05:00:58.156][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.157][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.158][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.159][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 05:00:58.160][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 05:00:58.161][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 05:00:58.162][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.163][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.164][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.165][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 05:00:58.166][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 05:00:58.167][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 05:00:58.168][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.168][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.169][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.170][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 05:00:58.171][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 05:00:58.172][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.173][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.174][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.175][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 05:00:58.176][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 05:00:58.177][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 05:00:58.178][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.180][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.181][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 05:00:58.182][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 05:00:58.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.185][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.DEBUG[2023-04-12 05:00:58.186][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 05:00:58.187][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 05:00:58.188][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 05:00:58.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.191][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.192][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 05:00:58.193][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 05:00:58.194][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 05:00:58.195][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 05:00:58.196][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 05:00:58.197][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 05:00:58.198][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.199][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.200][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[2023-04-12 05:00:58.201][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 05:00:58.202][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 05:00:58.203][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.204][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.205][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.206][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 05:00:58.207][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 05:00:58.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.208][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.209][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.210][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 05:00:58.211][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 05:00:58.212][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.214][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.215][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 05:00:58.216][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 05:00:58.217][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.219][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.220][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 05:00:58.221][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 05:00:58.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.222][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.223][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.224][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 05:00:58.225][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 05:00:58.230][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 05:00:58.231][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.232][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.233][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.234][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 05:00:58.235][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 05:00:58.236][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 05:00:58.237][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.239][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.240][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 05:00:58.242][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.243][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 05:00:58.244][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.245][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:00:58.246][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.247][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.248][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.249][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.250][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 05:00:58.251][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:00:58.252][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.253][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 05:00:58.254][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:00:58.255][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.256][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.257][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 05:00:58.257][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 05:00:58.257][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 05:00:58.257][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 05:00:58.257][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 05:00:58.258][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:00:58.259][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.260][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.261][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:00:58.262][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.262][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.263][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.264][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.265][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:00:58.266][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:00:58.267][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.268][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.269][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 05:00:58.271][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.272][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 05:00:58.273][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.274][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:00:58.275][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.276][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.277][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.278][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.279][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 05:00:58.280][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:00:58.281][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.282][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 05:00:58.283][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:00:58.284][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.285][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.286][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 05:00:58.286][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 05:00:58.286][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 05:00:58.286][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 05:00:58.286][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 05:00:58.287][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:00:58.288][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.289][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.290][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:00:58.291][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.292][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.293][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.294][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.295][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:00:58.296][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:00:58.297][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.298][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.299][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 05:00:58.301][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.302][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 05:00:58.303][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.304][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:00:58.305][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.306][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.307][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.308][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.309][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 05:00:58.310][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:00:58.311][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.312][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 05:00:58.313][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:00:58.313][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.314][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.315][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.316][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:00:58.317][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.318][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.319][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:00:58.320][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.321][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.322][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.323][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.324][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:00:58.325][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:00:58.326][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.327][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.328][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 05:00:58.330][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.331][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 05:00:58.332][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.333][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:00:58.334][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.335][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.336][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.337][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.338][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 05:00:58.339][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:00:58.340][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.341][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 05:00:58.342][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:00:58.343][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.344][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.345][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.346][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:00:58.347][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.348][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.349][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:00:58.350][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.351][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.354][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.355][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.356][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:00:58.357][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:00:58.358][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.359][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.360][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 05:00:58.361][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.362][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.363][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.364][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.365][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.365][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.366][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[2023-04-12 05:00:58.367][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.368][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.369][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.370][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.371][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.372][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.373][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.373][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.374][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.375][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.376][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.377][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.378][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.379][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.380][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.381][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.381][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.382][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.383][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.384][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.385][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.386][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.387][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.388][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.388][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.389][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.390][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.391][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.392][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.393][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.393][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.394][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.395][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.396][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.397][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.397][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.398][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.399][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.400][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.401][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.402][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.438][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.439][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.440][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.441][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.442][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.443][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.444][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.444][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.445][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.446][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.447][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.448][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.448][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.449][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.450][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.451][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.452][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.452][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.453][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.454][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.455][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.456][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.457][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.457][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[2023-04-12 05:00:58.458][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.459][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.460][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.460][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.461][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.462][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.463][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.464][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.464][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.465][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.466][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.467][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.468][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.468][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.469][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.470][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 05:00:58.471][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 05:00:58.473][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 05:00:58.474][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 05:00:58.475][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 05:00:58.477][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 05:00:58.478][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 05:00:58.479][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 05:00:58.480][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 05:00:58.481][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 05:00:58.483][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 05:00:58.484][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 05:00:58.485][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 05:00:58.486][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 05:00:58.488][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 05:00:58.489][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 05:00:58.490][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 05:00:58.491][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 05:00:58.493][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 05:00:58.494][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 05:00:58.495][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 05:00:58.496][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 05:00:58.497][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 05:00:58.499][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 05:00:58.500][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 05:00:58.501][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 05:00:58.502][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 05:00:58.504][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 05:00:58.505][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 05:00:58.506][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 05:00:58.507][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 05:00:58.509][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 05:00:58.510][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 05:00:58.511][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 05:00:58.512][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 05:00:58.514][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 05:00:58.515][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 05:00:58.516][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 05:00:58.517][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 05:00:58.519][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 05:00:58.520][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 05:00:58.521][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 05:00:58.522][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 05:00:58.524][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 05:00:58.525][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 05:00:58.526][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 05:00:58.528][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 05:00:58.529][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 05:00:58.530][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 05:00:58.531][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 05:00:58.533][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 05:00:58.534][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 05:00:58.535][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 05:00:58.536][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 05:00:58.537][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 05:00:58.539][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 05:00:58.540][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 05:00:58.541][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 05:00:58.542][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 05:00:58.544][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 05:00:58.545][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 05:00:58.546][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 05:00:58.548][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 05:00:58.549][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 05:00:58.550][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 05:00:58.552][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 05:00:58.553][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 05:00:58.554][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 05:00:58.555][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 05:00:58.557][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 05:00:58.558][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 05:00:58.560][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 05:00:58.561][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 05:00:58.562][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 05:00:58.564][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 05:00:58.565][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 05:00:58.566][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 05:00:58.568][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 05:00:58.569][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 05:00:58.570][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 05:00:58.572][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 05:00:58.573][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 05:00:58.574][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 05:00:58.576][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 05:00:58.577][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 05:00:58.578][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 05:00:58.579][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.580][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.581][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.582][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.582][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.583][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.584][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.585][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.586][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.587][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.588][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.588][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.589][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.590][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.591][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.592][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.593][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.593][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.594][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.595][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.596][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.597][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.598][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.598][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.599][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.600][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.601][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.602][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.603][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.604][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.604][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.605][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.606][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.607][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.608][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.609][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.610][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.610][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.611][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.612][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.613][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.614][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.615][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.616][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.616][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.617][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.618][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.619][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.620][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.621][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.621][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.622][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.623][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.DEBUG[2023-04-12 05:00:58.624][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.625][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.626][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.626][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.627][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.628][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.629][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.630][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.631][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.632][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.632][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.633][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.634][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.635][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.639][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.640][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.641][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.642][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.643][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.643][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.644][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.645][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.646][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.647][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.648][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.649][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.651][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.652][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.652][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.653][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.654][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.655][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.658][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.658][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.659][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.660][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.661][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.662][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.663][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.664][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.664][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.665][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.666][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.667][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.668][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.669][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.670][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.671][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.672][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.672][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.673][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.674][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.675][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.676][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.677][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.678][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.678][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.679][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.680][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.681][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.682][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:00:58.683][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:00:58.684][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:00:58.685][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:00:58.685][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:00:58.686][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:00:58.687][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:00:58.689][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-12 05:00:58.690][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 05:00:58.692][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.693][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.694][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.695][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:00:58.696][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.697][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.698][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.699][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.700][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 05:00:58.701][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:00:58.702][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.703][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-12 05:00:58.704][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-12 05:00:58.705][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-12 05:00:58.706][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 05:00:58.707][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 05:00:58.707][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 05:00:58.708][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:00:58.709][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.709][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.710][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:00:58.711][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:00:58.712][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:00:58.713][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:00:58.714][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 05:00:58.714][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-12 05:00:58.715][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:00:58.716][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:00:58.717][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 05:00:58.717][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:00:58.719][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-12 05:00:58.720][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 05:00:58.723][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 05:00:58.724][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-12 05:00:58.725][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 05:00:58.727][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-12 05:00:58.728][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-12 05:00:58.729][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-12 05:00:58.730][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-12 05:00:58.731][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-12 05:00:58.733][biodb::testThat]
biodb.INFO [2023-04-12 05:00:58.734][biodb::testThat] Running test function test_wsLmsdRecord_searchByName (" wsLmsdRecord() can search by name. ").
biodb.INFO [2023-04-12 05:00:58.735][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:00:58.736][biodb::testThat]
biodb.DEBUG[2023-04-12 05:00:58.740][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[2023-04-12 05:00:58.744][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:00:58.745][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:00:58.747][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride".
biodb.TRACE[2023-04-12 05:00:59.729][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=anhydride).
biodb.DEBUG[2023-04-12 05:01:00.439][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:00.450][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.content"
biodb.TRACE[2023-04-12 05:01:00.464][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cfd52aa1c2e3525a5defd7b7e8bd8bb8.request"
biodb.DEBUG[2023-04-12 05:01:00.478][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.DEBUG[2023-04-12 05:01:00.482][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:01:00.483][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:01:00.485][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&Name=fatty".
biodb.TRACE[2023-04-12 05:01:01.491][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[2023-04-12 05:01:02.212][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:02.224][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.content"
biodb.TRACE[2023-04-12 05:01:02.241][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/4ae22a112f570b93d2a956448ab71bd0.request"
biodb.INFO [2023-04-12 05:01:02.259][biodb::testThat]
biodb.INFO [2023-04-12 05:01:02.261][biodb::testThat] Running test function test_wsLmsdRecord (" Test web service wsLmsdRecord. ").
biodb.INFO [2023-04-12 05:01:02.263][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:01:02.264][biodb::testThat]
biodb.INFO [2023-04-12 05:01:02.313][biodb::testThat]
biodb.INFO [2023-04-12 05:01:02.315][biodb::testThat] Running test function test_wsLmsdSearch (" Test web service wsLmsdSearch. ").
biodb.INFO [2023-04-12 05:01:02.316][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:01:02.318][biodb::testThat]
biodb.DEBUG[2023-04-12 05:01:02.324][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[2023-04-12 05:01:02.329][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:01:02.331][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:01:02.334][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.TRACE[2023-04-12 05:01:02.851][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001).
biodb.DEBUG[2023-04-12 05:01:03.381][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:03.395][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content"
biodb.TRACE[2023-04-12 05:01:03.418][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.request"
biodb.DEBUG[2023-04-12 05:01:03.431][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&LMID=LMSL02000001".
biodb.DEBUG[2023-04-12 05:01:03.437][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 05:01:03.440][cch$loadFileContent] Trying to load 1 files from cache: [1]: "cb051dd8deddba61124ac06645747646".
biodb.TRACE[2023-04-12 05:01:03.443][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 05:01:03.445][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/cb051dd8deddba61124ac06645747646.content".
biodb.DEBUG[2023-04-12 05:01:03.455][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.DEBUG[2023-04-12 05:01:03.462][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:01:03.464][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:01:03.468][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&OutputType=TSV&LMID=LMSL02000001".
biodb.TRACE[2023-04-12 05:01:03.985][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[2023-04-12 05:01:04.510][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:04.522][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.content"
biodb.TRACE[2023-04-12 05:01:04.538][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/9edcc233717c530cf0cbf5f73b9c3fc7.request"
biodb.DEBUG[2023-04-12 05:01:04.550][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[2023-04-12 05:01:04.555][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:01:04.557][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:01:04.559][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid".
biodb.TRACE[2023-04-12 05:01:05.919][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid).
biodb.DEBUG[2023-04-12 05:01:09.365][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:09.407][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.content"
biodb.TRACE[2023-04-12 05:01:09.420][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/be9130a77f849b73da505cd10830451e.request"
biodb.DEBUG[2023-04-12 05:01:09.546][self$getBiodb()$getRequestScheduler( ...] Getting content of get URL request "https://www.lipidmaps.org/data/structure/LMSDSearch.php?Mode=ProcessStrSearch&OutputMode=File&Name=acid&ExactMass=60.8&ExactMassOffSet=6".
biodb.DEBUG[2023-04-12 05:01:09.550][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:01:09.551][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:01:09.553][private$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[2023-04-12 05:01:10.839][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[2023-04-12 05:01:14.430][self$getBiodb()$getRequestScheduler( ...] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:14.446][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.content"
biodb.TRACE[2023-04-12 05:01:14.473][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/6821b039f49696a2484834eb67daa971.request"
biodb.INFO [2023-04-12 05:01:14.604][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 05:01:14.606][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-12 05:01:14.608][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-12 05:01:14.609][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 05:01:14.610][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:14.611][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:14.612][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.614][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.615][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.616][FUN] Functions in observer BiodbConfig: [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 [2023-04-12 05:01:14.621][biodb::testContext]
biodb.INFO [2023-04-12 05:01:14.622][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 05:01:14.623][biodb::testContext] Test context - Some other custom tests
biodb.INFO [2023-04-12 05:01:14.625][biodb::testContext] ********************************************************************************
biodb.INFO [2023-04-12 05:01:14.626][biodb::testContext]
biodb.INFO [2023-04-12 05:01:14.632][private$loadBiodbPkgsDefinitions] Loading definitions from package biodb version 1.7.0.
biodb.DEBUG[2023-04-12 05:01:14.634][self$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodb/definitions.yml".
biodb.DEBUG[2023-04-12 05:01:14.640][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 05:01:14.641][self$getConfig()$define] Define config key allow.huge.downloads.
biodb.DEBUG[2023-04-12 05:01:14.643][self$set] Set key allow.huge.downloads to TRUE.
biodb.DEBUG[2023-04-12 05:01:14.644][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.645][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.646][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.647][self$getConfig()$define] Define config key autoload.extra.pkgs.
biodb.DEBUG[2023-04-12 05:01:14.648][self$set] Set key autoload.extra.pkgs to TRUE.
biodb.DEBUG[2023-04-12 05:01:14.649][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.650][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.652][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.653][self$getConfig()$define] Define config key cache.all.requests.
biodb.DEBUG[2023-04-12 05:01:14.654][self$set] Set key cache.all.requests to TRUE.
biodb.DEBUG[2023-04-12 05:01:14.655][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.656][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.657][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.658][self$getConfig()$define] Define config key cache.directory.
biodb.DEBUG[2023-04-12 05:01:14.660][self$getConfig()$define] Define config key cache.read.only.
biodb.DEBUG[2023-04-12 05:01:14.661][self$set] Set key cache.read.only to FALSE.
biodb.DEBUG[2023-04-12 05:01:14.662][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.663][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.665][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.666][self$getConfig()$define] Define config key cache.subfolders.
biodb.DEBUG[2023-04-12 05:01:14.667][self$getConfig()$define] Define config key cache.system.
biodb.DEBUG[2023-04-12 05:01:14.668][self$set] Set key cache.system to TRUE.
biodb.DEBUG[2023-04-12 05:01:14.669][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.670][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.671][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.673][self$getConfig()$define] Define config key use.cache.for.local.db.
biodb.DEBUG[2023-04-12 05:01:14.674][self$set] Set key use.cache.for.local.db to FALSE.
biodb.DEBUG[2023-04-12 05:01:14.675][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.676][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.677][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.678][self$getConfig()$define] Define config key dwnld.chunk.size.
biodb.DEBUG[2023-04-12 05:01:14.679][self$getConfig()$define] Define config key dwnld.timeout.
biodb.DEBUG[2023-04-12 05:01:14.680][self$set] Set key dwnld.timeout to 3600.
biodb.DEBUG[2023-04-12 05:01:14.681][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.682][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.683][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.684][self$getConfig()$define] Define config key compute.fields.
biodb.DEBUG[2023-04-12 05:01:14.686][self$set] Set key compute.fields to TRUE.
biodb.DEBUG[2023-04-12 05:01:14.687][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.688][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.689][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.690][self$getConfig()$define] Define config key factory.cache.
biodb.DEBUG[2023-04-12 05:01:14.691][self$getConfig()$define] Define config key force.locale.
biodb.DEBUG[2023-04-12 05:01:14.692][self$set] Set key force.locale to TRUE.
biodb.DEBUG[2023-04-12 05:01:14.693][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.694][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.695][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.696][self$getConfig()$define] Define config key longterm.cache.subfolder.
biodb.DEBUG[2023-04-12 05:01:14.697][self$getConfig()$define] Define config key msg.caution.lvl.
biodb.DEBUG[2023-04-12 05:01:14.698][self$getConfig()$define] Define config key msg.debug.lvl.
biodb.DEBUG[2023-04-12 05:01:14.700][self$getConfig()$define] Define config key msg.info.lvl.
biodb.DEBUG[2023-04-12 05:01:14.701][self$getConfig()$define] Define config key multival.field.sep.
biodb.DEBUG[2023-04-12 05:01:14.702][self$set] Set key multival.field.sep to ";".
biodb.DEBUG[2023-04-12 05:01:14.703][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.704][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.705][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[2023-04-12 05:01:14.706][self$getConfig()$define] Define config key intra.field.name.sep.
biodb.DEBUG[2023-04-12 05:01:14.707][self$set] Set key intra.field.name.sep to ".".
biodb.DEBUG[2023-04-12 05:01:14.708][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.709][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.710][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.711][self$getConfig()$define] Define config key entries.sep.
biodb.DEBUG[2023-04-12 05:01:14.713][self$set] Set key entries.sep to "|".
biodb.DEBUG[2023-04-12 05:01:14.714][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.715][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.716][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.717][self$getConfig()$define] Define config key offline.
biodb.DEBUG[2023-04-12 05:01:14.718][self$set] Set key offline to FALSE.
biodb.DEBUG[2023-04-12 05:01:14.719][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.720][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.721][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.722][self$getConfig()$define] Define config key persistent.cache.impl.
biodb.DEBUG[2023-04-12 05:01:14.724][self$set] Set key persistent.cache.impl to "custom".
biodb.DEBUG[2023-04-12 05:01:14.725][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.726][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.727][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.728][self$getConfig()$define] Define config key proton.mass.
biodb.DEBUG[2023-04-12 05:01:14.730][self$set] Set key proton.mass to 1.0072765.
biodb.DEBUG[2023-04-12 05:01:14.731][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.732][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.733][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.735][self$getConfig()$define] Define config key shortterm.cache.subfolder.
biodb.DEBUG[2023-04-12 05:01:14.736][self$getConfig()$define] Define config key svn.binary.path.
biodb.DEBUG[2023-04-12 05:01:14.742][self$set] Set key svn.binary.path to "".
biodb.DEBUG[2023-04-12 05:01:14.744][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.746][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.747][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.749][self$getConfig()$define] Define config key test.functions.
biodb.DEBUG[2023-04-12 05:01:14.751][self$getConfig()$define] Define config key useragent.
biodb.DEBUG[2023-04-12 05:01:14.752][self$set] Set key useragent to "R Bioconductor biodb library.".
biodb.DEBUG[2023-04-12 05:01:14.754][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.755][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.756][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.758][self$getDbsInfo()$define] Define connector comp.csv.file.
biodb.DEBUG[2023-04-12 05:01:14.761][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.763][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields.".
biodb.DEBUG[2023-04-12 05:01:14.764][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.766][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:01:14.767][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.768][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.770][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.771][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.773][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 05:01:14.774][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:01:14.776][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.777][self$setPropertyValue] Setting property "name" to "Compound CSV File".
biodb.DEBUG[2023-04-12 05:01:14.778][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:01:14.780][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.781][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.783][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 05:01:14.783][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 05:01:14.783][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 05:01:14.783][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 05:01:14.783][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 05:01:14.784][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:01:14.785][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.787][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.788][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:01:14.789][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.790][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.792][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.793][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.794][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:01:14.796][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:01:14.797][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.798][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.800][self$getDbsInfo()$define] Define connector comp.sqlite.
biodb.DEBUG[2023-04-12 05:01:14.803][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.805][self$setPropertyValue] Setting property "description" to "A connector to handle a compound database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 05:01:14.806][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.807][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:01:14.809][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.810][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.812][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.813][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.814][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 05:01:14.816][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:01:14.817][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.818][self$setPropertyValue] Setting property "name" to "Compound SQLite".
biodb.DEBUG[2023-04-12 05:01:14.820][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:01:14.821][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.822][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.823][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 05:01:14.823][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 05:01:14.823][self$setPropertyValue] Setting property "searchable.fields" to "molecular.mass".
biodb.DEBUG[2023-04-12 05:01:14.823][self$setPropertyValue] Setting property "searchable.fields" to "average.mass".
biodb.DEBUG[2023-04-12 05:01:14.823][self$setPropertyValue] Setting property "searchable.fields" to "nominal.mass".
biodb.DEBUG[2023-04-12 05:01:14.825][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:01:14.826][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.827][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.828][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:01:14.829][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.831][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.832][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.833][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.834][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:01:14.836][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:01:14.837][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.838][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.840][self$getDbsInfo()$define] Define connector mass.csv.file.
biodb.DEBUG[2023-04-12 05:01:14.843][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.844][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside a CSV file. It is possible to choose the separator for the CSV file, as well as match the column names with the biodb entry fields..".
biodb.DEBUG[2023-04-12 05:01:14.846][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.847][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:01:14.848][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.850][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.851][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.853][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.854][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 05:01:14.856][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:01:14.857][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.859][self$setPropertyValue] Setting property "name" to "Mass spectra CSV File".
biodb.DEBUG[2023-04-12 05:01:14.861][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:01:14.862][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.864][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.865][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.867][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:01:14.868][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.870][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.871][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:01:14.873][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.874][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.875][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.876][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.878][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:01:14.879][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:01:14.880][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.882][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.883][self$getDbsInfo()$define] Define connector mass.sqlite.
biodb.DEBUG[2023-04-12 05:01:14.886][self$setPropertyValue] Setting property "compound.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.887][self$setPropertyValue] Setting property "description" to "A connector to handle a mass spectra database stored inside an SQLite file.".
biodb.DEBUG[2023-04-12 05:01:14.888][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.889][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:01:14.890][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.892][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.893][self$setPropertyValue] Setting property "editable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.894][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.895][self$setPropertyValue] Setting property "entry.content.type" to "list".
biodb.DEBUG[2023-04-12 05:01:14.897][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:01:14.898][self$setPropertyValue] Setting property "mass.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.899][self$setPropertyValue] Setting property "name" to "Mass spectra SQLite".
biodb.DEBUG[2023-04-12 05:01:14.901][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:01:14.902][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.904][self$setPropertyValue] Setting property "remote" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:14.905][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.906][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:01:14.907][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.908][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.909][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:01:14.910][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:14.912][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:14.913][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:01:14.914][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.915][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:01:14.916][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:01:14.917][self$setPropertyValue] Setting property "writable" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:14.918][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:14.920][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 05:01:14.921][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.922][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[2023-04-12 05:01:14.923][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.924][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.925][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.926][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.928][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.929][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.930][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.931][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.932][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.933][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.934][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.935][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.936][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.937][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.938][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.939][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.941][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.942][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.943][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.944][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.945][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.946][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.947][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.991][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.992][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[2023-04-12 05:01:14.993][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.994][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:14.995][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:14.996][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:14.997][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:14.998][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:14.999][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.000][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.001][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.002][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.003][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.004][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.005][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.006][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.007][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[2023-04-12 05:01:15.008][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.009][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.010][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.011][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.012][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[2023-04-12 05:01:15.013][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.014][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.015][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.016][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.017][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.018][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.019][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.020][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.021][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.021][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[2023-04-12 05:01:15.022][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.023][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.024][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.025][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.026][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.027][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.028][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.029][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.030][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.031][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.032][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.033][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.034][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.035][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.036][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.037][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.038][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.040][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.042][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.044][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[2023-04-12 05:01:15.045][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.046][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.046][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.047][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.048][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.049][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.050][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.051][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.052][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.053][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.054][self$getEntryFields()$define] Define field accession.
biodb.DEBUG[2023-04-12 05:01:15.057][self$getEntryFields()$define] Define field description.
biodb.DEBUG[2023-04-12 05:01:15.059][self$getEntryFields()$define] Define field name.
biodb.DEBUG[2023-04-12 05:01:15.060][self$getEntryFields()$define] Define field cas.id.
biodb.DEBUG[2023-04-12 05:01:15.061][self$getEntryFields()$define] Define field chebi.id.
biodb.DEBUG[2023-04-12 05:01:15.063][self$getEntryFields()$define] Define field chemspider.id.
biodb.DEBUG[2023-04-12 05:01:15.064][self$getEntryFields()$define] Define field comp.csv.file.id.
biodb.DEBUG[2023-04-12 05:01:15.065][self$getEntryFields()$define] Define field comp.sqlite.id.
biodb.DEBUG[2023-04-12 05:01:15.067][self$getEntryFields()$define] Define field expasy.enzyme.id.
biodb.DEBUG[2023-04-12 05:01:15.068][self$getEntryFields()$define] Define field hmdb.metabolites.id.
biodb.DEBUG[2023-04-12 05:01:15.069][self$getEntryFields()$define] Define field kegg.compound.id.
biodb.DEBUG[2023-04-12 05:01:15.071][self$getEntryFields()$define] Define field kegg.genes.id.
biodb.DEBUG[2023-04-12 05:01:15.072][self$getEntryFields()$define] Define field mass.csv.file.id.
biodb.DEBUG[2023-04-12 05:01:15.073][self$getEntryFields()$define] Define field mass.sqlite.id.
biodb.DEBUG[2023-04-12 05:01:15.074][self$getEntryFields()$define] Define field ncbi.gene.id.
biodb.DEBUG[2023-04-12 05:01:15.076][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 05:01:15.077][self$getEntryFields()$define] Define field compound.id.
biodb.DEBUG[2023-04-12 05:01:15.078][self$getEntryFields()$define] Define field average.mass.
biodb.DEBUG[2023-04-12 05:01:15.080][self$getEntryFields()$define] Define field molecular.mass.
biodb.DEBUG[2023-04-12 05:01:15.081][self$getEntryFields()$define] Define field monoisotopic.mass.
biodb.DEBUG[2023-04-12 05:01:15.082][self$getEntryFields()$define] Define field nominal.mass.
biodb.DEBUG[2023-04-12 05:01:15.084][self$getEntryFields()$define] Define field peak.attr.
biodb.DEBUG[2023-04-12 05:01:15.085][self$getEntryFields()$define] Define field peak.comp.
biodb.DEBUG[2023-04-12 05:01:15.086][self$getEntryFields()$define] Define field peak.error.ppm.
biodb.DEBUG[2023-04-12 05:01:15.088][self$getEntryFields()$define] Define field peak.formula.
biodb.DEBUG[2023-04-12 05:01:15.089][self$getEntryFields()$define] Define field peak.intensity.
biodb.DEBUG[2023-04-12 05:01:15.090][self$getEntryFields()$define] Define field peak.mass.
biodb.DEBUG[2023-04-12 05:01:15.092][self$getEntryFields()$define] Define field peak.mztheo.
biodb.DEBUG[2023-04-12 05:01:15.093][self$getEntryFields()$define] Define field peak.mzexp.
biodb.DEBUG[2023-04-12 05:01:15.094][self$getEntryFields()$define] Define field peak.mz.
biodb.DEBUG[2023-04-12 05:01:15.096][self$getEntryFields()$define] Define field peak.relative.intensity.
biodb.DEBUG[2023-04-12 05:01:15.097][self$getEntryFields()$define] Define field peaks.
biodb.DEBUG[2023-04-12 05:01:15.098][self$getEntryFields()$define] Define field chrom.col.constructor.
biodb.DEBUG[2023-04-12 05:01:15.099][self$getEntryFields()$define] Define field chrom.col.diameter.
biodb.DEBUG[2023-04-12 05:01:15.101][self$getEntryFields()$define] Define field chrom.col.id.
biodb.DEBUG[2023-04-12 05:01:15.102][self$getEntryFields()$define] Define field chrom.col.length.
biodb.DEBUG[2023-04-12 05:01:15.103][self$getEntryFields()$define] Define field chrom.col.method.protocol.
biodb.DEBUG[2023-04-12 05:01:15.105][self$getEntryFields()$define] Define field chrom.col.name.
biodb.DEBUG[2023-04-12 05:01:15.106][self$getEntryFields()$define] Define field chrom.flow.gradient.
biodb.DEBUG[2023-04-12 05:01:15.107][self$getEntryFields()$define] Define field chrom.flow.rate.
biodb.DEBUG[2023-04-12 05:01:15.108][self$getEntryFields()$define] Define field chrom.rt.
biodb.DEBUG[2023-04-12 05:01:15.110][self$getEntryFields()$define] Define field chrom.rt.max.
biodb.DEBUG[2023-04-12 05:01:15.111][self$getEntryFields()$define] Define field chrom.rt.min.
biodb.DEBUG[2023-04-12 05:01:15.112][self$getEntryFields()$define] Define field chrom.rt.unit.
biodb.DEBUG[2023-04-12 05:01:15.114][self$getEntryFields()$define] Define field chrom.solvent.
biodb.DEBUG[2023-04-12 05:01:15.115][self$getEntryFields()$define] Define field aa.seq.
biodb.DEBUG[2023-04-12 05:01:15.116][self$getEntryFields()$define] Define field aa.seq.length.
biodb.DEBUG[2023-04-12 05:01:15.118][self$getEntryFields()$define] Define field aa.seq.location.
biodb.DEBUG[2023-04-12 05:01:15.119][self$getEntryFields()$define] Define field nt.seq.
biodb.DEBUG[2023-04-12 05:01:15.120][self$getEntryFields()$define] Define field nt.seq.length.
biodb.DEBUG[2023-04-12 05:01:15.122][self$getEntryFields()$define] Define field ec.
biodb.DEBUG[2023-04-12 05:01:15.123][self$getEntryFields()$define] Define field organism.
biodb.DEBUG[2023-04-12 05:01:15.125][self$getEntryFields()$define] Define field pathway.class.
biodb.DEBUG[2023-04-12 05:01:15.126][self$getEntryFields()$define] Define field catalytic.activity.
biodb.DEBUG[2023-04-12 05:01:15.127][self$getEntryFields()$define] Define field cofactor.
biodb.DEBUG[2023-04-12 05:01:15.129][self$getEntryFields()$define] Define field gene.symbol.
biodb.DEBUG[2023-04-12 05:01:15.130][self$getEntryFields()$define] Define field charge.
biodb.DEBUG[2023-04-12 05:01:15.132][self$getEntryFields()$define] Define field comp.iupac.name.allowed.
biodb.DEBUG[2023-04-12 05:01:15.133][self$getEntryFields()$define] Define field comp.iupac.name.cas.
biodb.DEBUG[2023-04-12 05:01:15.135][self$getEntryFields()$define] Define field comp.iupac.name.pref.
biodb.DEBUG[2023-04-12 05:01:15.136][self$getEntryFields()$define] Define field comp.iupac.name.syst.
biodb.DEBUG[2023-04-12 05:01:15.138][self$getEntryFields()$define] Define field comp.iupac.name.trad.
biodb.DEBUG[2023-04-12 05:01:15.139][self$getEntryFields()$define] Define field comp.super.class.
biodb.DEBUG[2023-04-12 05:01:15.141][self$getEntryFields()$define] Define field equation.
biodb.DEBUG[2023-04-12 05:01:15.142][self$getEntryFields()$define] Define field formula.
biodb.DEBUG[2023-04-12 05:01:15.143][self$getEntryFields()$define] Define field composition.
biodb.DEBUG[2023-04-12 05:01:15.145][self$getEntryFields()$define] Define field inchi.
biodb.DEBUG[2023-04-12 05:01:15.146][self$getEntryFields()$define] Define field inchikey.
biodb.DEBUG[2023-04-12 05:01:15.148][self$getEntryFields()$define] Define field logp.
biodb.DEBUG[2023-04-12 05:01:15.149][self$getEntryFields()$define] Define field ms.level.
biodb.DEBUG[2023-04-12 05:01:15.151][self$getEntryFields()$define] Define field ms.mode.
biodb.DEBUG[2023-04-12 05:01:15.152][self$getEntryFields()$define] Define field msdev.
biodb.DEBUG[2023-04-12 05:01:15.154][self$getEntryFields()$define] Define field msdevtype.
biodb.DEBUG[2023-04-12 05:01:15.155][self$getEntryFields()$define] Define field msprecannot.
biodb.DEBUG[2023-04-12 05:01:15.156][self$getEntryFields()$define] Define field msprecmz.
biodb.DEBUG[2023-04-12 05:01:15.158][self$getEntryFields()$define] Define field mstype.
biodb.DEBUG[2023-04-12 05:01:15.159][self$getEntryFields()$define] Define field nb.compounds.
biodb.DEBUG[2023-04-12 05:01:15.161][self$getEntryFields()$define] Define field nb.peaks.
biodb.DEBUG[2023-04-12 05:01:15.162][self$getEntryFields()$define] Define field products.
biodb.DEBUG[2023-04-12 05:01:15.163][self$getEntryFields()$define] Define field smiles.
biodb.DEBUG[2023-04-12 05:01:15.165][self$getEntryFields()$define] Define field smiles.canonical.
biodb.DEBUG[2023-04-12 05:01:15.166][self$getEntryFields()$define] Define field smiles.isomeric.
biodb.DEBUG[2023-04-12 05:01:15.167][self$getEntryFields()$define] Define field substrates.
biodb.DEBUG[2023-04-12 05:01:15.169][initialize] Created successfully new BiodbMain instance.
biodb.DEBUG[2023-04-12 05:01:15.171][initialize] This is biodb version 1.7.0.
biodb.DEBUG[2023-04-12 05:01:15.172][notifyObservers] Notify observers for notifyNewObservers.
biodb.DEBUG[2023-04-12 05:01:15.173][FUN] Trying to call function notifyNewObservers on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.174][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.174][FUN] Trying to call function notifyNewObservers on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.175][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.176][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.177][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.178][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.179][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.180][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.181][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.182][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.183][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.184][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.185][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.185][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.186][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.187][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.188][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.189][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.190][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.191][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.192][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.193][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.194][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.194][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[2023-04-12 05:01:15.195][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.196][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.197][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.198][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.199][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.200][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.201][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.202][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.203][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.204][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.205][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.206][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.206][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.207][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[2023-04-12 05:01:15.208][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.209][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.210][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.211][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.212][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.213][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.214][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[2023-04-12 05:01:15.215][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.216][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.217][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.218][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.219][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.220][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.221][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.222][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.223][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.224][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.225][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.226][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.227][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.227][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[2023-04-12 05:01:15.228][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.229][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.230][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.231][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.232][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.233][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.234][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[2023-04-12 05:01:15.235][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.236][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.237][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.238][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.239][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.240][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.241][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.242][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.243][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.244][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.245][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.246][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.247][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.248][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.249][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.250][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.250][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.251][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.252][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.253][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.254][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.DEBUG[2023-04-12 05:01:15.255][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.256][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.257][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.258][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.259][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.260][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.261][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.262][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.263][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.264][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.265][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.266][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.266][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.267][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.268][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.269][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.270][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.271][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.272][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.273][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.274][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.275][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.276][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.277][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.278][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.278][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.279][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.280][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.281][notifyObservers] Notify observers for notifyCfgUpdate.
biodb.DEBUG[2023-04-12 05:01:15.282][FUN] Trying to call function notifyCfgUpdate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:15.283][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:15.284][FUN] Trying to call function notifyCfgUpdate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:15.285][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:15.286][FUN] Trying to call function notifyCfgUpdate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:15.287][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:15.289][biodb$loadDefinitions] Load definitions from file "/home/biocbuild/bbs-3.17-bioc/R/site-library/biodbLipidmaps/definitions.yml".
biodb.DEBUG[2023-04-12 05:01:15.290][self$getDbsInfo()$define] Define connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 05:01:15.293][self$setPropertyValue] Setting property "compound.db" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:15.294][self$setPropertyValue] Setting property "description" to "NA".
biodb.DEBUG[2023-04-12 05:01:15.295][self$setPropertyValue] Setting property "disabled" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:15.296][self$setPropertyValue] Setting property "disabling.reason" to "".
biodb.DEBUG[2023-04-12 05:01:15.297][self$setPropertyValue] Setting property "downloadable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:15.298][self$setPropertyValue] Setting property "dwnld.ext" to "NA".
biodb.DEBUG[2023-04-12 05:01:15.300][self$setPropertyValue] Setting property "editable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:15.301][self$setPropertyValue] Setting property "entry.content.encoding" to "NA".
biodb.DEBUG[2023-04-12 05:01:15.302][self$setPropertyValue] Setting property "entry.content.type" to "tsv".
biodb.DEBUG[2023-04-12 05:01:15.303][self$setPropertyValue] Setting property "matching.fields" to "c("peak.mztheo", "peak.mzexp")".
biodb.DEBUG[2023-04-12 05:01:15.304][self$setPropertyValue] Setting property "mass.db" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:15.305][self$setPropertyValue] Setting property "name" to "LIPID MAPS Structure".
biodb.DEBUG[2023-04-12 05:01:15.306][self$setPropertyValue] Setting property "package" to "biodb".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "LM_ID".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "CHEBI_ID".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "HMDBID".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "KEGG_ID".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "PUBCHEM_COMPOUND_ID".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "SYSTEMATIC_NAME".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "MASS".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "FORMULA".
biodb.DEBUG[2023-04-12 05:01:15.307][self$setPropertyValue] Setting property "parsing.expr" to "COMMON_NAME".
biodb.DEBUG[2023-04-12 05:01:15.308][self$setPropertyValue] Setting property "remote" to "TRUE".
biodb.DEBUG[2023-04-12 05:01:15.310][self$setPropertyValue] Setting property "searchable.fields" to "name".
biodb.DEBUG[2023-04-12 05:01:15.310][self$setPropertyValue] Setting property "searchable.fields" to "monoisotopic.mass".
biodb.DEBUG[2023-04-12 05:01:15.311][self$setPropertyValue] Setting property "scheduler.n" to "1".
biodb.DEBUG[2023-04-12 05:01:15.312][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:15.313][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:15.314][self$setPropertyValue] Setting property "scheduler.t" to "1".
biodb.DEBUG[2023-04-12 05:01:15.315][self$setPropertyValue] Notifying observers about frequency change.
biodb.DEBUG[2023-04-12 05:01:15.316][notifyObservers] Notify observers for notifyConnSchedulerFrequencyUpdated.
biodb.DEBUG[2023-04-12 05:01:15.317][self$setPropertyValue] Setting property "token" to "NA".
biodb.DEBUG[2023-04-12 05:01:15.318][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 05:01:15.318][self$setPropertyValue] Setting property "urls" to "https://www.lipidmaps.org/databases/lmsd/".
biodb.DEBUG[2023-04-12 05:01:15.319][self$setPropertyValue] Notifying observers about URLs change.
biodb.DEBUG[2023-04-12 05:01:15.320][notifyObservers] Notify observers for notifyConnUrlsUpdated.
biodb.DEBUG[2023-04-12 05:01:15.321][self$setPropertyValue] Setting property "writable" to "FALSE".
biodb.DEBUG[2023-04-12 05:01:15.322][self$setPropertyValue]
biodb.DEBUG[2023-04-12 05:01:15.324][self$getEntryFields()$define] Define field lipidmaps.structure.id.
biodb.DEBUG[2023-04-12 05:01:15.325][self$getEntryFields()$define] Define field ncbi.pubchem.comp.id.
biodb.DEBUG[2023-04-12 05:01:15.329][initialize] Initialize connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 05:01:15.330][initialize] Register connector lipidmaps.structure with the request scheduler
biodb.DEBUG[2023-04-12 05:01:15.331][private$bdb$getRequestScheduler()$re ...] Register connector lipidmaps.structure.
biodb.DEBUG[2023-04-12 05:01:15.333][private$addConnectorRules] Create new rule for URL "www.lipidmaps.org" of connector "lipidmaps.structure".
biodb.DEBUG[2023-04-12 05:01:15.334][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-12 05:01:15.335][self$setFrequency] t=1.000000, n=1.000000
biodb.DEBUG[2023-04-12 05:01:15.337][rule$addConnector] Connector "lipidmaps.structure" is already listed in rule "www.lipidmaps.org".
biodb.DEBUG[2023-04-12 05:01:15.338][biodb$getFactory()$createConn] Creating new connector lipidmaps.structure for database class lipidmaps.structure .
biodb.INFO [2023-04-12 05:01:15.340][biodb::testThat]
biodb.INFO [2023-04-12 05:01:15.341][biodb::testThat] Running test function test_noOtherConnNeeded (" No other connector is needed. ").
biodb.INFO [2023-04-12 05:01:15.342][biodb::testThat] --------------------------------------------------------------------------------
biodb.INFO [2023-04-12 05:01:15.343][biodb::testThat]
biodb.DEBUG[2023-04-12 05:01:15.348][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[2023-04-12 05:01:15.352][self$getBiodb()$getRequestScheduler( ...] Loading content of request from cache.
biodb.TRACE[2023-04-12 05:01:15.354][cch$loadFileContent] Trying to load 1 files from cache: [1]: "13e15253cf65619ae7a700f5534f6030".
biodb.TRACE[2023-04-12 05:01:15.373][cch$loadFileContent] file.exist = [1]: "TRUE".
biodb.TRACE[2023-04-12 05:01:15.430][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/13e15253cf65619ae7a700f5534f6030.content".
biodb.DEBUG[2023-04-12 05:01:16.322][private$loadEntries] Creating entries from ids [2]: "LMFA00000001, LMFA00000002".
biodb.DEBUG[2023-04-12 05:01:16.323][conn$getEntryContent] Get LIPID MAPS Structure entry content(s) for 2 id(s)...
biodb.TRACE[2023-04-12 05:01:16.325][cch$loadFileContent] Trying to load 2 files from cache: [2]: "LMFA00000001, LMFA00000002".
biodb.TRACE[2023-04-12 05:01:16.327][cch$loadFileContent] file.exist = [2]: "FALSE, TRUE".
biodb.TRACE[2023-04-12 05:01:16.329][loadFileContents] Loaded 1 files from cache: [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000002.tsv".
biodb.DEBUG[2023-04-12 05:01:16.330][conn$getEntryContent] 1 LIPID MAPS Structure entry content(s) loaded from cache.
biodb.DEBUG[2023-04-12 05:01:16.331][conn$getEntryContent] 1 entry content(s) need to be fetched from LIPID MAPS Structure database "https://www.lipidmaps.org/data/".
biodb.DEBUG[2023-04-12 05:01:16.332][conn$getEntryContent] dwnld.chunk.size=NA
biodb.DEBUG[2023-04-12 05:01:16.333][conn$getEntryContent] 1 chunk(s) to download.
biodb.DEBUG[2023-04-12 05:01:16.337][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:01:16.338][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:16.339][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:16.345][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:16.346][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:16.348][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:16.349][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.DEBUG[2023-04-12 05:01:16.350][scheduler$sendRequest] Getting content of get URL request "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.DEBUG[2023-04-12 05:01:16.353][private$doSendRequestLoop] Request header is: "".
biodb.DEBUG[2023-04-12 05:01:16.354][private$doSendRequestLoop] Request body is "".
biodb.TRACE[2023-04-12 05:01:16.356][private$doSendRequestOnce] Sent URL is "https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv".
biodb.TRACE[2023-04-12 05:01:17.076][getRCurlRequestResult] Using RCurl package for sending request (https://www.lipidmaps.org/databases/lmsd/LMFA00000001?format=tsv).
biodb.DEBUG[2023-04-12 05:01:17.787][scheduler$sendRequest] Saving content of request to cache.
biodb.TRACE[2023-04-12 05:01:17.795][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.content"
biodb.TRACE[2023-04-12 05:01:17.807][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/f441f4b59d8c1fbcb63f4f502d20d459.request"
biodb.TRACE[2023-04-12 05:01:17.818][private$doSaveContentToFile] Saving to cache [1]: "/home/biocbuild/.cache/R/biodb/lipidmaps.structure-ccd4263a0c0fd7a1cb4329cb919bd54b/LMFA00000001.tsv"
biodb.DEBUG[2023-04-12 05:01:17.822][conn$getEntryContent] Now 0 id(s) left to be retrieved...
biodb.DEBUG[2023-04-12 05:01:17.840][self$createEntryFromContent] Creating LIPID MAPS Structure entries from 2 content(s).
biodb.DEBUG[2023-04-12 05:01:17.842][self$createEntryFromContent] Parsing 2 LIPID MAPS Structure entries.
biodb.DEBUG[2023-04-12 05:01:17.843][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:01:17.844][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:17.845][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:17.851][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:17.852][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:17.854][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:17.855][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 05:01:17.859][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:17.861][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:17.862][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.863][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.864][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:17.865][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:17.866][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.867][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.872][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:17.873][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:17.874][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.875][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.876][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:17.877][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:17.878][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.879][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.883][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:01:17.885][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:01:17.886][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.887][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.888][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:01:17.889][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:01:17.890][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.891][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.892][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:17.893][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:17.894][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.895][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.897][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:17.898][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:17.899][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.900][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.904][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:17.905][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:17.906][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.907][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.909][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:17.910][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:17.911][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.912][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.916][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 05:01:17.918][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:17.919][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.920][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.921][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 05:01:17.922][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:17.923][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.924][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.929][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:17.930][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:17.931][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.932][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.934][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:17.935][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:17.936][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.937][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.942][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.943][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.944][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.945][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.946][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.947][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.948][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.950][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.954][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 05:01:17.955][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.956][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.957][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.959][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 05:01:17.960][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.961][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.962][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.963][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.964][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.965][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.966][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.968][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.969][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.970][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.971][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.972][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 05:01:17.973][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.974][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.975][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.980][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.981][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.982][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.984][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.985][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.986][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.987][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.988][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.989][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.990][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.991][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.992][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.994][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.995][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:17.996][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:17.997][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:17.998][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:17.999][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.000][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.001][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.006][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.007][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.008][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.009][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.010][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.011][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.013][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.014][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.015][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.016][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.017][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.018][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.019][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.020][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.022][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.023][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.024][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.025][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.026][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.027][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.028][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.030][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.031][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.032][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.033][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.034][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.035][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.036][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 05:01:18.041][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:01:18.042][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:18.043][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:18.049][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:18.050][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:18.051][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:18.052][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 05:01:18.057][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.058][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.059][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.060][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.061][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.063][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.064][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.065][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.069][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.071][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.072][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.073][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.074][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.076][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.077][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.078][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.082][self$getBiodb()$getEntryFields()$get] Asked field names are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:01:18.083][self$getBiodb()$getEntryFields()$get] Realnames of fields are: hmdb.metabolites.id.
biodb.TRACE[2023-04-12 05:01:18.084][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.085][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.087][self$getBiodb()$getEntryFields()$get] Asked field names are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:01:18.088][self$getBiodb()$getEntryFields()$get] Realnames of fields are: kegg.compound.id.
biodb.TRACE[2023-04-12 05:01:18.089][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.090][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.091][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.092][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.093][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.094][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.095][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.096][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.097][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.098][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.154][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.156][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.157][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.158][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.159][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.161][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.162][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.163][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.167][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 05:01:18.169][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.170][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.171][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.172][self$getBiodb()$getEntryFields()$get] Asked field names are: exact.mass.
biodb.TRACE[2023-04-12 05:01:18.173][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.174][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.175][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.179][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.181][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.182][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.183][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.184][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.185][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.186][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.187][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.191][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.193][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.194][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.195][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.196][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.197][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.198][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.199][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.204][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 05:01:18.205][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.206][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.207][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.208][self$getBiodb()$getEntryFields()$get] Asked field names are: synonyms.
biodb.TRACE[2023-04-12 05:01:18.209][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.210][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.212][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.213][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.214][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.215][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.216][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.217][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.218][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.219][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.220][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.221][self$getBiodb()$getEntryFields()$get] Asked field names are: SYNONYMS.
biodb.TRACE[2023-04-12 05:01:18.223][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.224][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.225][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.229][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.231][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.232][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.233][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.234][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.235][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.236][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.237][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.238][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.239][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.240][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.241][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.243][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.244][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.245][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.246][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.247][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.248][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.249][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.250][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.251][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.252][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.253][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.254][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.255][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.256][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.257][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.258][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.263][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.264][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.265][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.266][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.268][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.269][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.270][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.271][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.272][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.273][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.274][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.275][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.276][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.278][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.279][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.280][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.281][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.282][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.283][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.284][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.285][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.286][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.287][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.288][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.DEBUG[2023-04-12 05:01:18.289][self$createEntryFromContent] Accession numbers: LMFA00000001, LMFA00000002.
biodb.DEBUG[2023-04-12 05:01:18.292][conn$getBiodb()$entriesToDataframe] 2 entrie(s) to convert in data frame.
biodb.DEBUG[2023-04-12 05:01:18.295][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:01:18.296][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:18.297][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:18.304][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:18.306][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:18.307][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:18.308][FUN] Functions in observer BiodbConfig: [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[2023-04-12 05:01:18.310][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.311][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.313][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.314][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.315][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.316][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.317][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.318][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.319][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 05:01:18.320][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 05:01:18.321][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.322][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.323][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 05:01:18.325][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 05:01:18.326][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.327][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.328][private$selectFields] Fields none
biodb.TRACE[2023-04-12 05:01:18.329][private$selectFields]
biodb.TRACE[2023-04-12 05:01:18.330][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-12 05:01:18.331][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 05:01:18.332][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-12 05:01:18.333][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.334][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.335][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.336][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.337][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.338][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.339][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.340][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.341][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.342][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.343][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.344][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.345][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.346][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.347][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.348][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.349][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.351][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.352][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.353][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.354][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.355][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.356][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.357][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.358][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.359][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.360][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.361][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.362][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.363][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.364][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.365][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.366][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.367][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.369][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.370][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.371][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.372][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.374][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.375][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.376][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.377][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.378][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.380][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.381][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.382][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.384][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.385][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.386][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.388][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.389][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.390][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.391][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.393][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.394][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.395][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.396][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.398][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.399][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.400][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.401][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.403][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.404][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.405][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.407][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-12 05:01:18.408][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-12 05:01:18.409][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.411][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.412][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.413][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.415][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.416][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.417][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.418][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.420][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.421][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.422][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.424][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.425][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.426][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.427][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.429][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.430][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.431][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.433][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.434][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.435][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.437][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.438][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.439][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.441][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.442][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.443][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.444][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.446][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.447][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.448][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.449][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.450][private$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[2023-04-12 05:01:18.452][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.453][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.454][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.455][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.456][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.458][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.459][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.460][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.461][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.462][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.464][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.465][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.467][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.468][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.470][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.471][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.472][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.474][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.475][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.476][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.478][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.479][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.481][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.482][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.484][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.485][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.486][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.488][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.489][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.491][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.492][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.493][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.495][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.497][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.498][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.499][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.500][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.501][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.503][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.504][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.505][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.507][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.508][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.509][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.510][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.511][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.512][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.513][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.514][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.516][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.517][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.518][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.519][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.521][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.522][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.523][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.524][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.526][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.527][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.528][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.529][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.531][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.532][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.533][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.535][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.536][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.538][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.539][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.540][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.541][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.542][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.543][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.545][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.546][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.547][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.548][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.549][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.550][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.551][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.552][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.553][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.555][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.556][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.557][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.558][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.560][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.561][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.584][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.586][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.587][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.588][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.589][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.590][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.591][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.592][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.593][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.600][private$entriesToListOfDataframes] Entry converted to data frame: [1, 8]: [accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, ...] [LMFA00000001, 178363, 10930192, 2-methoxy-12-methyloctadec-17-en-5-ynoyl anhydride, 626.491025, ...].
biodb.DEBUG[2023-04-12 05:01:18.602][notifyObservers] Notify observers for notifyProgress.
biodb.DEBUG[2023-04-12 05:01:18.603][FUN] Trying to call function notifyProgress on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:18.604][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:18.610][FUN] Trying to call function notifyProgress on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:18.611][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:18.612][FUN] Trying to call function notifyProgress on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:18.613][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
biodb.TRACE[2023-04-12 05:01:18.616][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.617][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.618][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.619][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.620][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.621][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mz.
biodb.TRACE[2023-04-12 05:01:18.622][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.623][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.624][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mzexp.
biodb.TRACE[2023-04-12 05:01:18.625][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mzexp.
biodb.TRACE[2023-04-12 05:01:18.626][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.627][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.628][self$getBiodb()$getEntryFields()$get] Asked field names are: peak.mztheo.
biodb.TRACE[2023-04-12 05:01:18.629][self$getBiodb()$getEntryFields()$get] Realnames of fields are: peak.mztheo.
biodb.TRACE[2023-04-12 05:01:18.630][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.631][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.632][private$selectFields] Fields none
biodb.TRACE[2023-04-12 05:01:18.632][private$selectFields]
biodb.TRACE[2023-04-12 05:01:18.633][private$selectFields] Fields is null: TRUE
biodb.TRACE[2023-04-12 05:01:18.634][private$selectFields] Fields.type is null: TRUE
biodb.TRACE[2023-04-12 05:01:18.635][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-12 05:01:18.636][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.637][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.638][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.639][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.640][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.641][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.642][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.643][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.644][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.645][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.646][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.647][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.648][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.649][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.650][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.651][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.652][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.653][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.654][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.655][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.656][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.657][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.658][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.659][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.660][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.661][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.662][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.663][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.664][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.665][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.666][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.667][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.668][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.669][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.670][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.671][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.672][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.673][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.674][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.675][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.676][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.677][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.678][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.679][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.680][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.681][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.682][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.683][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.684][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.685][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.686][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.687][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.688][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.689][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.690][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.691][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.692][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.693][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.694][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.695][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.696][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.697][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.698][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.699][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.700][private$selectFields] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-12 05:01:18.701][private$organizeFieldsByGroups] Fields [8]: "accession, chebi.id, ncbi.pubchem.comp.id, comp.iupac.name.syst, monoisotopic.mass, formula, name, lipidmaps.structure.id"
biodb.TRACE[2023-04-12 05:01:18.702][ef$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.703][ef$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.704][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.705][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.706][ef$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.708][ef$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.709][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.710][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.711][ef$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.712][ef$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.713][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.714][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.715][ef$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.716][ef$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.717][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.718][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.719][ef$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.720][ef$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.721][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.722][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.723][ef$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.724][ef$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.725][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.726][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.727][ef$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.728][ef$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.729][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.730][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.731][ef$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.732][ef$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.733][ef$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.734][ef$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.735][private$organizeFieldsByGroups] Groups [2]: "c("accession", "chebi.id", "ncbi.pubchem.comp.id", "comp.iupac.name.syst", "monoisotopic.mass", "formula", "name", "lipidmaps.structure.id"), list()"
biodb.TRACE[2023-04-12 05:01:18.736][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.737][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.738][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.739][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.740][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.741][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.742][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.743][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.744][self$getBiodb()$getEntryFields()$get] Asked field names are: accession.
biodb.TRACE[2023-04-12 05:01:18.745][self$getBiodb()$getEntryFields()$get] Realnames of fields are: accession.
biodb.TRACE[2023-04-12 05:01:18.746][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.747][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.749][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.750][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.753][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.755][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.756][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.757][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.758][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.759][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.761][self$getBiodb()$getEntryFields()$get] Asked field names are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.762][self$getBiodb()$getEntryFields()$get] Realnames of fields are: chebi.id.
biodb.TRACE[2023-04-12 05:01:18.762][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.763][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.765][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.766][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.767][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.768][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.769][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.770][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.771][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.772][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.773][self$getBiodb()$getEntryFields()$get] Asked field names are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.774][self$getBiodb()$getEntryFields()$get] Realnames of fields are: ncbi.pubchem.comp.id.
biodb.TRACE[2023-04-12 05:01:18.775][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.776][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.777][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.778][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.780][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.781][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.782][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.783][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.784][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.785][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.786][self$getBiodb()$getEntryFields()$get] Asked field names are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.787][self$getBiodb()$getEntryFields()$get] Realnames of fields are: comp.iupac.name.syst.
biodb.TRACE[2023-04-12 05:01:18.788][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.789][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.790][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.791][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.792][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.793][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.794][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.795][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.796][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.797][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.798][self$getBiodb()$getEntryFields()$get] Asked field names are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.799][self$getBiodb()$getEntryFields()$get] Realnames of fields are: monoisotopic.mass.
biodb.TRACE[2023-04-12 05:01:18.800][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.801][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.802][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.803][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.804][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.805][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.806][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.807][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.808][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.809][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.810][self$getBiodb()$getEntryFields()$get] Asked field names are: formula.
biodb.TRACE[2023-04-12 05:01:18.811][self$getBiodb()$getEntryFields()$get] Realnames of fields are: formula.
biodb.TRACE[2023-04-12 05:01:18.812][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.813][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.814][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.816][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.817][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.818][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.819][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.820][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.821][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.822][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.823][self$getBiodb()$getEntryFields()$get] Asked field names are: name.
biodb.TRACE[2023-04-12 05:01:18.824][self$getBiodb()$getEntryFields()$get] Realnames of fields are: name.
biodb.TRACE[2023-04-12 05:01:18.825][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.825][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.827][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.828][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.829][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.830][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.831][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.832][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.833][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.833][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.834][self$getBiodb()$getEntryFields()$get] Asked field names are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.836][self$getBiodb()$getEntryFields()$get] Realnames of fields are: lipidmaps.structure.id.
biodb.TRACE[2023-04-12 05:01:18.836][self$getBiodb()$getEntryFields()$get] 1 fields were returned.
biodb.TRACE[2023-04-12 05:01:18.837][self$getBiodb()$getEntryFields()$get] fields variable is a list.
biodb.TRACE[2023-04-12 05:01:18.842][private$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[2023-04-12 05:01:18.843][private$entriesToListOfDataframes] Converted 2 entry/ies to data frame(s).
biodb.DEBUG[2023-04-12 05:01:18.844][conn$getBiodb()$entriesToDataframe] Merging data frames with a singleentry each into a single data frame with all entries.
biodb.INFO [2023-04-12 05:01:18.848][biodb$terminate] Closing BiodbMain instance...
biodb.DEBUG[2023-04-12 05:01:18.849][private$conn[[conn]]$.__enclos_env__ ...] Unregister connector lipidmaps.structure from the request scheduler
biodb.INFO [2023-04-12 05:01:18.850][self$deleteConn] Connector "lipidmaps.structure" deleted.
biodb.DEBUG[2023-04-12 05:01:18.851][notifyObservers] Notify observers for terminate.
biodb.DEBUG[2023-04-12 05:01:18.852][FUN] Trying to call function terminate on observer BiodbTestMsgAck.
biodb.DEBUG[2023-04-12 05:01:18.853][FUN] Functions in observer BiodbTestMsgAck: [4]: ".__enclos_env__, clone, notifyProgress, initialize".
biodb.DEBUG[2023-04-12 05:01:18.854][FUN] Trying to call function terminate on observer BiodbEntryFields.
biodb.DEBUG[2023-04-12 05:01:18.855][FUN] Functions in observer BiodbEntryFields: [15]: ".__enclos_env__, clone, terminate, define, print, getDatabaseIdField, getFieldNames, get, getRealName, checkIsDefined, isDefined, formatName, isAlias, notifyCfgUpdate, initialize".
biodb.DEBUG[2023-04-12 05:01:18.856][FUN] Trying to call function terminate on observer BiodbConfig.
biodb.DEBUG[2023-04-12 05:01:18.857][FUN] Functions in observer BiodbConfig: [21]: ".__enclos_env__, clone, terminate, notifyNewObservers, define, getAssocEnvVar, listKeys, print, disable, enable, reset, set, get, isEnabled, isDefined, hasKey, getDefaultValue, getDescription, getTitle, getKeys, initialize".
[ FAIL 0 | WARN 0 | SKIP 0 | PASS 169 ]
>
> proc.time()
user system elapsed
22.194 2.660 148.069
biodbLipidmaps.Rcheck/biodbLipidmaps-Ex.timings
| name | user | system | elapsed | |
| LipidmapsStructureConn | 0.701 | 0.027 | 0.727 | |
| LipidmapsStructureEntry | 0.171 | 0.004 | 0.175 | |